[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[maria goranovic]

Hello List

I want to change an ASP to a D-ASP. I think it should be possible by simply
changing 2 improper values around the chiral carbon to their opposite sign.
Instead of making a brand new residue, I thought I would take the topology
of an ASP generated by pdb2gmx, and simply change values manually in the
resulting .itp. However, this is not possible because gromacs wants to read
the dihedral parameters from the ffbonded.itp file. Is it possible for me to
explicitly state the parameters for these two dihedrals in my d-asp.itp
file? This will be the fastest solution to the problem because it precludes
making a new residue or defining new atoms types and so on. With the CHARMM
force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which we
are used to for gromos topologies.

The mailing list search function was down, so I could not explore prior
messages about this.

--

Maria

-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[Tsjerk Wassenaar]

Hi Maria,

The CHARMM force field is an all-atom one. That means it does not
require improper dihedrals to maintain chirality. If you have a D-ASP
in your structure file, you can rename it to ASP and just run pdb2gmx.
Mind not to regenerate hydrogens in that case, or make sure to modify
the hydrogen position for the D amino acids afterwards, to set the
proper chirality.

Hope it helps,

Tsjerk

On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
 wrote:
> Hello List
> I want to change an ASP to a D-ASP. I think it should be possible by simply
> changing 2 improper values around the chiral carbon to their opposite sign.
> Instead of making a brand new residue, I thought I would take the topology
> of an ASP generated by pdb2gmx, and simply change values manually in the
> resulting .itp. However, this is not possible because gromacs wants to read
> the dihedral parameters from the ffbonded.itp file. Is it possible for me to
> explicitly state the parameters for these two dihedrals in my d-asp.itp
> file? This will be the fastest solution to the problem because it precludes
> making a new residue or defining new atoms types and so on. With the CHARMM
> force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which we
> are used to for gromos topologies.
> The mailing list search function was down, so I could not explore prior
> messages about this.
> --
> Maria
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)

[bipin singh]

Hello users,

Although there was already much discussion had been done on the procedure to
construct DCCM map from covar.dat(i.e. output from g_covar) but still I am
not clear
with the step wise procedure to calculate the correlation matrix from
covarience matrix(covar.dat).

1) It is stated in the previous posts that to calculate correlation matrix
we have to
divide each i,j-th element of the covariance matrix (covar.dat) by the sqrt
of the ii-th and jj-th diagonal
element, but how to get diagonal of a 865107X3 matrix???
2) As given in the manual the order of elements in covar.dat is is:
x1x1,x1y1, x1z1, x1x2, ...
But I am not clear which are i,j-th ,ii-th and jj-th elements in covar.dat.

My covarience matrix have  865107 rows and 3 columns and the total atoms are
537(sqrt( 865107 X 3) / 3=537 atoms)
Can anyone suggest how to transform the covar.dat into correlation matrix.
I am expecting the stepwise procedure to construct the correlation matrix
and not the theory behind it as it already stated in the
previous posts.

regards
Bipin
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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[maria goranovic]

Hi

Appreciate the quick help

I am sorry, this is not an improper, but a proper dihedral that holds the
chirality in place. Then the solution suggested by Meli would not work? I do
not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So
the question is simply how to set the proper chirality to a D-amino acid in
CHARMM.



Maria

On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar wrote:

> Hi Maria,
>
> The CHARMM force field is an all-atom one. That means it does not
> require improper dihedrals to maintain chirality. If you have a D-ASP
> in your structure file, you can rename it to ASP and just run pdb2gmx.
> Mind not to regenerate hydrogens in that case, or make sure to modify
> the hydrogen position for the D amino acids afterwards, to set the
> proper chirality.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
>  wrote:
> > Hello List
> > I want to change an ASP to a D-ASP. I think it should be possible by
> simply
> > changing 2 improper values around the chiral carbon to their opposite
> sign.
> > Instead of making a brand new residue, I thought I would take the
> topology
> > of an ASP generated by pdb2gmx, and simply change values manually in the
> > resulting .itp. However, this is not possible because gromacs wants to
> read
> > the dihedral parameters from the ffbonded.itp file. Is it possible for me
> to
> > explicitly state the parameters for these two dihedrals in my d-asp.itp
> > file? This will be the fastest solution to the problem because it
> precludes
> > making a new residue or defining new atoms types and so on. With the
> CHARMM
> > force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which
> we
> > are used to for gromos topologies.
> > The mailing list search function was down, so I could not explore prior
> > messages about this.
> > --
> > Maria
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[Tsjerk Wassenaar]

Hi Maria,

The general solution is to copy the entry in the .rtp file, modify the
dihedrals involved, and rename the entry to match the name used in the
coordinate (pdb) file. You may also need to copy the entries in the
.hdb file, as well as the .tdb files if it is a terminal residue.

Hope it helps,

Tsjerk

On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic
 wrote:
> Hi
> Appreciate the quick help
> I am sorry, this is not an improper, but a proper dihedral that holds the
> chirality in place. Then the solution suggested by Meli would not work? I do
> not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So
> the question is simply how to set the proper chirality to a D-amino acid in
> CHARMM.
>
>
> Maria
> On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar 
> wrote:
>>
>> Hi Maria,
>>
>> The CHARMM force field is an all-atom one. That means it does not
>> require improper dihedrals to maintain chirality. If you have a D-ASP
>> in your structure file, you can rename it to ASP and just run pdb2gmx.
>> Mind not to regenerate hydrogens in that case, or make sure to modify
>> the hydrogen position for the D amino acids afterwards, to set the
>> proper chirality.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
>>  wrote:
>> > Hello List
>> > I want to change an ASP to a D-ASP. I think it should be possible by
>> > simply
>> > changing 2 improper values around the chiral carbon to their opposite
>> > sign.
>> > Instead of making a brand new residue, I thought I would take the
>> > topology
>> > of an ASP generated by pdb2gmx, and simply change values manually in the
>> > resulting .itp. However, this is not possible because gromacs wants to
>> > read
>> > the dihedral parameters from the ffbonded.itp file. Is it possible for
>> > me to
>> > explicitly state the parameters for these two dihedrals in my d-asp.itp
>> > file? This will be the fastest solution to the problem because it
>> > precludes
>> > making a new residue or defining new atoms types and so on. With the
>> > CHARMM
>> > force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which
>> > we
>> > are used to for gromos topologies.
>> > The mailing list search function was down, so I could not explore prior
>> > messages about this.
>> > --
>> > Maria
>> >
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>> > --
>> > gmx-users mailing list    gmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Citation for NICS

[Sergio Manzetti]

Hello everyone, is this citation proper for citing NICS?

I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of
Measuring Nuclear Magnetic Moment". *Physical
Review
* *53*: 318. doi :
10.1103/PhysRev.53.318 .
PMID
 9981980 .
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[gmx-users] units for atomic coordinates in traj.xtc? nm?

[Jennifer Williams]

A very quick question.

Can someone confirm that atomic coordinates are stored as in the  
traj.xtc file in units of nm (as opposed to Angstroms)?


I am trying to figure out whether or not in the g_msd program reads in  
nm or Angstroms. The standard output of the xy graph is nm2 and ps. I  
can't see that the units are being divided by 10 in the g_msd code so  
I am guessing the traj.xtc feeds in the units in nm.  Just want to be  
sure...


Thanks




--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: [gmx-users] units for atomic coordinates in traj.xtc? nm?

[Justin A. Lemkul]

Jennifer Williams wrote:

A very quick question.

Can someone confirm that atomic coordinates are stored as in the 
traj.xtc file in units of nm (as opposed to Angstroms)?


I am trying to figure out whether or not in the g_msd program reads in 
nm or Angstroms. The standard output of the xy graph is nm2 and ps. I 
can't see that the units are being divided by 10 in the g_msd code so I 
am guessing the traj.xtc feeds in the units in nm.  Just want to be sure...


Standard units are given in Chapter 2 of the manual.  For distances, 
coordinates, etc everything is in nm.


You can also use gmxdump to convince yourself of this fact.

-Justin



Thanks






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Antw: [gmx-users] Citation for NICS

[Emanuel Peter]

Hello,

Why do you ask this ?



>>> Sergio Manzetti  25.03.11 13.09 Uhr >>>
Hello everyone, is this citation proper for citing NICS?

I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of 
Measuring Nuclear Magnetic Moment". Physical Review 53: 318. 
doi:10.1103/PhysRev.53.318. PMID 9981980.

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Re: [gmx-users] Citation for NICS

[Sergio Manzetti]

Beacuse I want to cite NICS.

On Fri, Mar 25, 2011 at 8:56 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:

> Hello,
>
> Why do you ask this ?
>
>
>
> >>> Sergio Manzetti 25.03.11 13.09 Uhr >>>
>
> Hello everyone, is this citation proper for citing NICS?
>
> I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of
> Measuring Nuclear Magnetic Moment". *Physical 
> Review
> * *53*: 318. doi :
> 10.1103/PhysRev.53.318 . 
> PMID
>  9981980 .
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] Citation for NICS

[Justin A. Lemkul]

Sergio Manzetti wrote:

Beacuse I want to cite NICS.



Clearly.  But posing a question about experimental NMR techniques to the Gromacs 
software list is probably not the most efficient approach to getting an answer.


A quick Google search turns up numerous recent reviews about NICS.  Doubtless 
you'll find your answer there, and certainly much faster than waiting around for 
someone on a simulation list to (maybe) give an answer to an off-topic question 
about a 70-year old paper.


-Justin

On Fri, Mar 25, 2011 at 8:56 PM, Emanuel Peter 
> wrote:


Hello,

Why do you ask this ?



 >>> Sergio Manzetti 25.03.11 13.09  Uhr >>>

Hello everyone, is this citation proper for citing NICS?

I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New
Method of Measuring Nuclear Magnetic Moment". /Physical Review
/ *53*: 318. doi

:10.1103/PhysRev.53.318
. PMID
 9981980
.

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Carbohydrate simulation: problem with the terminal atoms

[Somaye Badieyan]

Hi everyone, 



I am using g53a6 force filed for the simulation of cellulose. However it seems
that parametrization works only for the sugar blocked linked together and no
terminal atoms for terminal residues are defined there (I mean the start and
end atom, H and O atom at the beginning linked to c4 and H atom at the last
Sugar residue linked to O1). I tried to solve the problem by making the
topology file removing the start OH and end H group from the initial PDB file 
to 
have the topology file made by g53a6 and later add the parameters of OH and H
to the topology file. The problem is at the time of minimization almost no
change in energy (not converged even after 7325 step) with the maximum force
(about 9e+03) on the H of new added OH group (the start OH group). and when I
checked the output of minimization step I found the HO position and C2 and C3,
O3 atoms are deformed and the defined angles/bonds/dihedral of this new OH are
not kept (the other H group the the other side, end, is fine). I know the
problem is due to the way I defined the parameters but I do not know what the
problem exactly is. Since the original topology file without the terminal atoms
start from 1, the terminal atoms are added at the end of gro file and topology
file (although OH group is part of first residue): 



the molecule is a cellotetetraose and here is the added part to top file (Atom
number: H at end: 57 ,  O at start:58,   H at start:59):



; residue 1001 GLCB rtp GLCB q 
0.0

 1   
CH1   1001   GLCB
C4  1 
0.332 13.019   ; qtot 0.232

 2   
CH1   1001   GLCB
C3  2 
0.232 13.019   ; qtot 0.464

 3
OA   1001   GLCB
O3  2
-0.642    15.9994   ; qtot -0.178


4  H  
1001   GLCB    HO3 
2   0.41 
1.008   ; qtot 0.232

        .

    .

    .

   
56 OA  
1004   GLCB O1
20 -0.642    15.9994   ; qtot
-0.20

    57 
H   1004   GLCB   
HO1 20 
0.282  1.008   ; qtot 0

;added later to 1000 GLCB

    58
OA   1001   GLCB
O4  1
-0.542    15.9994   ;

    59 
H   1001   GLCB   
HO4  1 
0.442  1.008   ;



[ bonds ]

;  ai    aj
funct   
c0   
c1    c2   
c3

    1 2
2    gb_26

    1    11
2    gb_26

.

.

.

  55    56 2   
gb_20

   56    57
2    gb_1

   58 1
2    gb_20

   58    59
2    gb_1



[ angles ]

;  ai    aj    ak
funct   
c0   
c1   
c2    c3

    2 1   
11 2    ga_8

    1 2
3 2    ga_9

    1 2
5 2    ga_8

.

.

.

   55    56   
57 2    ga_12

   11 1   
58 2    ga_9

   58 1
2 2    ga_9

    1    58   
59 2    ga_12



[ dihedrals ]

;  ai    aj    ak    al
funct   
c0   
c1   
c2   
c3   
c4    c5

   11 1
2 3 1    gd_17

   11 1
2 5 1    gd_34

    2 1   
11 8 1    gd_34

.

.

.

   59    58
1 2 1    gd_30

   58 1
2 3 1    gd_18

   58 1
2 5 1    gd_17

   58 1
11    8 1    gd_17



[ dihedrals ]

;  ai    aj    ak    al
funct   
c0   
c1   
c2    c3

.

.

.

   11 2   
58 1 2    gi_2





I prepare this parameters based on the other OH group in the sugars and
parameters of link oxygen (the shared oxygen at the position of glycosidic bond
that is expected to be O4 group of the next residue). 

 

I
did not use the PRODRG since i need 53a6 and I found for carbohydrate there is
too much different between the parameters in 53a6 and 43a1. Somewhere it ahs
been mentioned to change the terminal database file (.tdb), however I think it
may make the problem more complicated. 



Your help is appreciated.

-Somaye

 

...

Somayesadat Badieyan

PhD Candidate and Research Assistant 

Biological Syatems Engineering

201 Seitz Hall, Virginia Tech

Blacksburg,
VA 24060

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Re: [gmx-users] Carbohydrate simulation: problem with the terminal atoms

[nishap . patel]

I am not sure if you have looked through this paper, but it gives the  
parameters for sugars.


A new GROMOS force field for hexopyranose-based carbohydrates by RD Lins, 2005

A biomolecular force field based on the free enthalpy of hydration and  
solvation: The GROMOS force?field parameter sets 53A5 and 53A6- C  
Oostenbrink, 2004


Hope that helps.

Nisha P



Quoting Somaye Badieyan :


Hi everyone,



I am using g53a6 force filed for the simulation of cellulose.   
However it seems

that parametrization works only for the sugar blocked linked together and no
terminal atoms for terminal residues are defined there (I mean the start and
end atom, H and O atom at the beginning linked to c4 and H atom at the last
Sugar residue linked to O1). I tried to solve the problem by making the
topology file removing the start OH and end H group from the initial  
 PDB file to 

have the topology file made by g53a6 and later add the parameters of OH and H
to the topology file. The problem is at the time of minimization almost no
change in energy (not converged even after 7325 step) with the maximum force
(about 9e+03) on the H of new added OH group (the start OH group). and when I
checked the output of minimization step I found the HO position and   
C2 and C3,
O3 atoms are deformed and the defined angles/bonds/dihedral of this   
new OH are

not kept (the other H group the the other side, end, is fine). I know the
problem is due to the way I defined the parameters but I do not know what the
problem exactly is. Since the original topology file without the   
terminal atoms
start from 1, the terminal atoms are added at the end of gro file   
and topology

file (although OH group is part of first residue):



the molecule is a cellotetetraose and here is the added part to top   
file (Atom

number: H at end: 57 ,  O at start:58,   H at start:59):



; residue 1001 GLCB rtp GLCB q 
0.0

 1   
CH1   1001   GLCB
C4  1 
0.332 13.019   ; qtot 0.232

 2   
CH1   1001   GLCB
C3  2 
0.232 13.019   ; qtot 0.464

 3
OA   1001   GLCB
O3  2
-0.642    15.9994   ; qtot -0.178


4  H  
1001   GLCB    HO3 
2   0.41 
1.008   ; qtot 0.232

        .

    .

    .

   
56 OA  
1004   GLCB O1
20 -0.642    15.9994   ; qtot
-0.20

    57 
H   1004   GLCB   
HO1 20 
0.282  1.008   ; qtot 0

;added later to 1000 GLCB

    58
OA   1001   GLCB
O4  1
-0.542    15.9994   ;

    59 
H   1001   GLCB   
HO4  1 
0.442  1.008   ;



[ bonds ]

;  ai    aj
funct   
c0   
c1    c2   
c3

    1 2
2    gb_26

    1    11
2    gb_26

.

.

.

  55    56 2   
gb_20

   56    57
2    gb_1

   58 1
2    gb_20

   58    59
2    gb_1



[ angles ]

;  ai    aj    ak
funct   
c0   
c1   
c2    c3

    2 1   
11 2    ga_8

    1 2
3 2    ga_9

    1 2
5 2    ga_8

.

.

.

   55    56   
57 2    ga_12

   11 1   
58 2    ga_9

   58 1
2 2    ga_9

    1    58   
59 2    ga_12



[ dihedrals ]

;  ai    aj    ak    al
funct   
c0   
c1   
c2   
c3   
c4    c5

   11 1
2 3 1    gd_17

   11 1
2 5 1    gd_34

    2 1   
11 8 1    gd_34

.

.

.

   59    58
1 2 1    gd_30

   58 1
2 3 1    gd_18

   58 1
2 5 1    gd_17

   58 1
11    8 1    gd_17



[ dihedrals ]

;  ai    aj    ak    al
funct   
c0   
c1   
c2    c3

.

.

.

   11 2   
58 1 2    gi_2





I prepare this parameters based on the other OH group in the sugars and
parameters of link oxygen (the shared oxygen at the position of   
glycosidic bond

that is expected to be O4 group of the next residue).

 

I
did not use the PRODRG since i need 53a6 and I found for   
carbohydrate there is

too much different between the parameters in 53a6 and 43a1. Somewhere it ahs
been mentioned to change the terminal database file (.tdb), however   
I think it

may make the problem more complicated.



Your help is appreciated.

-Somaye

 

...

Somayesadat Badieyan

PhD Candidate and Research Assistant

Biological Syatems Engineering

201 Seitz Hall, Virginia Tech

Blacksburg,
VA 24060

...




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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[maria goranovic]

Yes, that would be the correct way to do this. I was hoping to take a
shorter route, and just modifying a couple of dihedrals in the topology
files output by pdb2gmx without having to make a new residue. Is that not
possible at all ?



On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar wrote:

> Hi Maria,
>
> The general solution is to copy the entry in the .rtp file, modify the
> dihedrals involved, and rename the entry to match the name used in the
> coordinate (pdb) file. You may also need to copy the entries in the
> .hdb file, as well as the .tdb files if it is a terminal residue.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic
>  wrote:
> > Hi
> > Appreciate the quick help
> > I am sorry, this is not an improper, but a proper dihedral that holds the
> > chirality in place. Then the solution suggested by Meli would not work? I
> do
> > not have a D-ASP. I in fact have an L-ASP which i want to convert to D.
> So
> > the question is simply how to set the proper chirality to a D-amino acid
> in
> > CHARMM.
> >
> >
> > Maria
> > On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar 
> > wrote:
> >>
> >> Hi Maria,
> >>
> >> The CHARMM force field is an all-atom one. That means it does not
> >> require improper dihedrals to maintain chirality. If you have a D-ASP
> >> in your structure file, you can rename it to ASP and just run pdb2gmx.
> >> Mind not to regenerate hydrogens in that case, or make sure to modify
> >> the hydrogen position for the D amino acids afterwards, to set the
> >> proper chirality.
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >>
> >> On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
> >>  wrote:
> >> > Hello List
> >> > I want to change an ASP to a D-ASP. I think it should be possible by
> >> > simply
> >> > changing 2 improper values around the chiral carbon to their opposite
> >> > sign.
> >> > Instead of making a brand new residue, I thought I would take the
> >> > topology
> >> > of an ASP generated by pdb2gmx, and simply change values manually in
> the
> >> > resulting .itp. However, this is not possible because gromacs wants to
> >> > read
> >> > the dihedral parameters from the ffbonded.itp file. Is it possible for
> >> > me to
> >> > explicitly state the parameters for these two dihedrals in my
> d-asp.itp
> >> > file? This will be the fastest solution to the problem because it
> >> > precludes
> >> > making a new residue or defining new atoms types and so on. With the
> >> > CHARMM
> >> > force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3
> which
> >> > we
> >> > are used to for gromos topologies.
> >> > The mailing list search function was down, so I could not explore
> prior
> >> > messages about this.
> >> > --
> >> > Maria
> >> >
> >> > --
> >> > Maria G.
> >> > Technical University of Denmark
> >> > Copenhagen
> >> >
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
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> Please don't post 

[gmx-users] flexible spc water model

[Nilesh Dhumal]

Hello,

I am want to use flexible spc water model for my simulation.

I define=-DFLEX_SPC in my mdp and mentioned  #include "spc.itp" in my .top
file.

Does it correct?


 I am using gromacs 4.0.7 version.
Thanks

Nilesh



dipcorr.pdf
Description: Adobe PDF document
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Re: [gmx-users] flexible spc water model

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

I am want to use flexible spc water model for my simulation.



Might I inquire as to why?  SPC was parameterized to be rigid, and as has been 
stated numerous times across the list, flexible water should not be used.



I define=-DFLEX_SPC in my mdp and mentioned  #include "spc.itp" in my .top
file.

Does it correct?



Presumably.  Check the post-processed topology that grompp gives you (-pp 
argument).

-Justin



 I am using gromacs 4.0.7 version.
Thanks

Nilesh




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_cluster segmentation fault

[Craig Kitchen]

Dear All,

When running g_cluster on a file generated with g_mdmat I receive a 
segmentation fault. I have tried different versions of Gromacs (4.0.5 and 
4.5.3) on different workstations with both large and small matrices - all 
without success.


I am calling g_cluster with:

g_cluster -dm dmat_1.xpm -cutoff 3.4 -g cluster_1.log

Whereupon I receive the error:

Using linkage method for clustering
Reading rms distance matrix 100%
Segmentation fault

The distance matrix (dmat_1.xpm) was generated with:

g_mdmat -f onlyba.gro -s onlyba.gro -t 4.0 -mean dmat_1.xpm

The configuration (onlyba.gro) and matrix file (dmat_1.xpm) are attached 
(and since they are short also pasted below).


Any help on this would be greatly appreciated!

Regards,

Craig

Craig Kitchen
Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge
CB2 1EW
UK




Generated by trjconv : Coarse-Grained Model of EAS Barrels and Loop 
Residues (including bonds) t= 0.0

 10
  1BA  BA1  44.780  21.592  37.304  0.0067  0.0035  0.0073
 29BA  BA2  12.191  38.323   0.704 -0.0084  0.0108 -0.0014
 57BA  BA3   2.092   9.298  47.957  0.0053 -0.0144  0.0053
 85BA  BA4  15.664  33.182  25.406  0.0291 -0.0067 -0.0069
113BA  BA5  47.194  32.613  24.031 -0.0146 -0.0132  0.0184
141BA  BA6  11.731  25.247  11.921 -0.0100 -0.0049  0.0025
169BA  BA7  33.751  20.349  25.599 -0.0103 -0.0131  0.0078
197BA  BA8   2.467  11.277  47.988 -0.0063  0.0188 -0.0001
225BA  BA9  25.948  26.283  35.007  0.0191  0.0058  0.0047
253BA  BA   10  26.103  27.621  36.697 -0.0057  0.0281 -0.0110
48.0  48.0  48.0


/* XPM */
/* Generated by g_mdmat */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title:   "Mean smallest distance" */
/* legend:  "Distance (nm)" */
/* x-label: "Residue Index" */
/* y-label: "Residue Index" */
/* type:"Continuous" */
static char *gromacs_xpm[] = {
"10 10   40 1",
"A  c #FF " /* "0" */,
"B  c #F8F8F8 " /* "0.103" */,
"C  c #F2F2F2 " /* "0.205" */,
"D  c #EBEBEB " /* "0.308" */,
"E  c #E5E5E5 " /* "0.41" */,
"F  c #DEDEDE " /* "0.513" */,
"G  c #D8D8D8 " /* "0.615" */,
"H  c #D1D1D1 " /* "0.718" */,
"I  c #CBCBCB " /* "0.821" */,
"J  c #C4C4C4 " /* "0.923" */,
"K  c #BEBEBE " /* "1.03" */,
"L  c #B7B7B7 " /* "1.13" */,
"M  c #B1B1B1 " /* "1.23" */,
"N  c #AA " /* "1.33" */,
"O  c #A3A3A3 " /* "1.44" */,
"P  c #9D9D9D " /* "1.54" */,
"Q  c #969696 " /* "1.64" */,
"R  c #909090 " /* "1.74" */,
"S  c #898989 " /* "1.85" */,
"T  c #838383 " /* "1.95" */,
"U  c #7C7C7C " /* "2.05" */,
"V  c #767676 " /* "2.15" */,
"W  c #6F6F6F " /* "2.26" */,
"X  c #696969 " /* "2.36" */,
"Y  c #626262 " /* "2.46" */,
"Z  c #5C5C5C " /* "2.56" */,
"a  c #55 " /* "2.67" */,
"b  c #4E4E4E " /* "2.77" */,
"c  c #484848 " /* "2.87" */,
"d  c #414141 " /* "2.97" */,
"e  c #3B3B3B " /* "3.08" */,
"f  c #343434 " /* "3.18" */,
"g  c #2E2E2E " /* "3.28" */,
"h  c #272727 " /* "3.38" */,
"i  c #212121 " /* "3.49" */,
"j  c #1A1A1A " /* "3.59" */,
"k  c #141414 " /* "3.69" */,
"l  c #0D0D0D " /* "3.79" */,
"m  c #070707 " /* "3.9" */,
"n  c #00 " /* "4" */,
/* x-axis:  1 2 3 4 5 6 7 8 9 10 */
/* y-axis:  1 2 3 4 5 6 7 8 9 10 */
"VA",
"AV",
"nnUAnn",
"nnAnnn",
"nA",
"An",
"nnnAnn",
"nnAUnn",
"nA",
"An"

onlyba.gro
Description: onlyba.gro


dmat_1.xpm
Description: dmat_1.xpm
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Re: [gmx-users] no output dgdl file

[Moeed]

Thank you Justin and Emanuel for helpful remarks. I am a little confused
what is the proper detailed procedure to perform FE using TI and BAR when
decoupling nonboded terms separately. I write down my understanding and
would appreciate your comments.

Summary:

TI: One needs to vary init_lambda (=native) from 0 to 10 (say 0.1
increments) and obtain 11 xvg files. (for simultaneous decoupling)

1- Here  foreign_lambda does not make sense as it pertains to BAR.
2- If one intends to do separate decoupling, for each native labmda run two
times with the appropriate couple-lambda0  &  couple-lambda1. For each
native lambda we end up with two xvg files. coul-0 to coul-11 and vdw-0 to
vdw-11. (actually I am not sure what is easiest way of summing up two
columns from coul-0 + vdw-0 ... aside from EXCEL..). Move the total sum at
each point to the file total-0 to total 11. Run g_average on each total-?
and perform numerical integration to get delta G or H.

BAR: Run 2*11 times with the following settings for appropriate
couple-lambda0  &  couple-lambda1 to get coul-0 to coul-11 and vdw-0 to
vdw-11.

Interval 1:
init_lambda = 0
foreign_lambda = 0.05

Interval 2:
init_lambda = 0.05
foreign_lambda = 0 0.1

Interval 3:
init_lambda = 0.1
foreign_lambda = 0.05 0.15


Add up coul-0+vdw-0 > total-0  (again I dont know the proper tool for adding
up columns)
.
.  (for intermedaite steps there are
3 columns to sum. one before and after native lambda)
.
> total 11


Run g_bar on total-?.xvg files.


1- I am wondering for each interval say

Interval 2:
init_lambda = 0.05
foreign_lambda = 0 0.1

how this foreign_lambda 0 is related to the init_lambda = 0 from interval 1
and the same for foreign_lambda = 0.1 in interval 2 and init_lambda = 0.1 in
interval 3? Is there a physical meaning?

2- If one needs to run multiple native lambda for both methods what is the
adnatage of BAR over TI. I thought using foreign_lambda facilitates FE
calculations in terms of amount of work but it seems it is only a different
method (BAR).

Thanks for your help.


>
> Emanuel Birru wrote:
>
>> Yeah, I am using IT and do analyse the result using another method not
>> bar. But I used g_bar when I was using the foreign_lambda and simulate
>> all in a single file. I have already sent my suspect few weeks back.
>>
>
> Is there an active redmine issue?  I cannot find any post from you in the
> list archive from the last few months.  What is the issue?
>
>
>  I am a bit confused on the g_bar part, when it says -f expects multiple
>> dhdl files. Do we need to run still multiple independent simulations
>> using different foreign_lambda values? I do not see why we should run
>> independent simulations, if we use for couple-lambda0 and couple-lambda1
>> vdw-q and none respectively.
>>
>>
> As I mentioned to the OP of this thread, simultaneous (de)coupling of vdW
> and Coulombic interactions is not stable.  The output energies are not
> trustworthy, in my experience due to physically unreasonable configurations
> and the potential for numerical singularities.
>
> The multiple files that g_bar expects are not simply from two separate
> processes, however.  It expects dhdl.xvg files from multiple values of
> native lambda that have corresponding foreign_lambda values in it, i.e.:
>
> Interval 1:
> init_lambda = 0
> foreign_lambda = 0.05
>
> Interval 2:
> init_lambda = 0.05
> foreign_lambda = 0 0.1
>
> Interval 3:
> init_lambda = 0.1
> foreign_lambda = 0.05 0.15
>
> etc.
>
> -Justin
>
>
>  For IT I am using 4.5.3 and it is working good so far.
>>
>> Cheers,
>>
>> -Original Message-
>> From: gmx-users-boun...@gromacs.org
>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
>> Sent: Thursday, 24 March 2011 1:36 PM
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] no output dgdl file
>>
>>
>>
>> Emanuel Birru wrote:
>>
>>> Hi Justin,
>>>
>>> It good that the issue is solved. As per my experience if you want to
>>>
>> do
>>
>>> a series of simulations it is not necessary to use foreign_lambda, for
>>> each simulation we can give different lambda values starting from 0 to
>>> 1( from fully interactive to non-interactive) no need of foreign_lamda
>>>
>>
>> This is certainly a viable method, but it is thermodynamic integration,
>> not BAR.   The purpose of lambda/foreign_lambda is to use the BAR method.
>>
>>  and certainly no need of generating dhdl.xvg to calculate FE. I think
>>> -dhdl is an optional it will not be generated just because
>>>
>> "free_energy
>>
>>> = yes" is present. The problem with the 4.5.3 is not the problem of
>>>
>>
>> It has always been my experience (in versions 3.3.3 and 4.5.3) that if
>> the free energy code is activated, this file is written.  I never specify
>> the
>> file names independently.
>>
>>  generating dhdl data by using single simulation with all
>>>
>> foreign_lambda
>>
>>> values. The problem is with g_bar, when I tried to

Re: [gmx-users] no output dgdl file

[Szilárd Páll]

> 1- I am wondering for each interval say
>
> Interval 2:
> init_lambda = 0.05
> foreign_lambda = 0 0.1
>
> how this foreign_lambda 0 is related to the init_lambda = 0 from interval 1
> and the same for foreign_lambda = 0.1 in interval 2 and init_lambda = 0.1 in
> interval 3? Is there a physical meaning?

Intermediate states are non-physical. For the details on how do
intermediate state contribute to the final free energy estimate, see
the original BAR paper [*].

> 2- If one needs to run multiple native lambda for both methods what is the
> adnatage of BAR over TI. I thought using foreign_lambda facilitates FE
> calculations in terms of amount of work but it seems it is only a different
> method (BAR).

Regarding 2), to summarize the advantage of BAR: it's been proved that
it's the best asymptotically unbiased method which the its greatest
strength.

In practice, unlike with TI where in order to sample efficiently you
need containment relationship between the "important" states of B wrt
the important states of A, for BAR good overlap is enough. Also, the
method itself provides with an estimate for overlap which gives a good
indication where you need more lambda points. Again, for details check
[*].

A few more points:
- You don't need all other states as foreign_lambda for a certain
lambda, but if you put them all there it won't hurt, but it will
increase your runtime. A rule of thumb often used is to use as foreign
lambdas a few lambda values around the respective lambda.
-  There is a very handy feature which makes possible writing the free
energy data to the binary edr files (separate_dhdl_file = no mdp
option). The advantages are much faster processing with g_bar and way
less disk usage (note that you can write energy frames relatively
rarely if you wish, while sampling the dhdl more often).


[*] Bennett, Efficient estimation of free energy differences from
Monte Carlo data; JCP (1976); 22:(2), 245-268.

--
Szilárd

>>
>>
>> Emanuel Birru wrote:
>>>
>>> Yeah, I am using IT and do analyse the result using another method not
>>> bar. But I used g_bar when I was using the foreign_lambda and simulate
>>> all in a single file. I have already sent my suspect few weeks back.
>>
>> Is there an active redmine issue?  I cannot find any post from you in the
>> list archive from the last few months.  What is the issue?
>>
>>> I am a bit confused on the g_bar part, when it says -f expects multiple
>>> dhdl files. Do we need to run still multiple independent simulations
>>> using different foreign_lambda values? I do not see why we should run
>>> independent simulations, if we use for couple-lambda0 and couple-lambda1
>>> vdw-q and none respectively.
>>>
>>
>> As I mentioned to the OP of this thread, simultaneous (de)coupling of vdW
>> and Coulombic interactions is not stable.  The output energies are not
>> trustworthy, in my experience due to physically unreasonable configurations
>> and the potential for numerical singularities.
>>
>> The multiple files that g_bar expects are not simply from two separate
>> processes, however.  It expects dhdl.xvg files from multiple values of
>> native lambda that have corresponding foreign_lambda values in it, i.e.:
>>
>> Interval 1:
>> init_lambda = 0
>> foreign_lambda = 0.05
>>
>> Interval 2:
>> init_lambda = 0.05
>> foreign_lambda = 0 0.1
>>
>> Interval 3:
>> init_lambda = 0.1
>> foreign_lambda = 0.05 0.15
>>
>> etc.
>>
>> -Justin
>>
>>> For IT I am using 4.5.3 and it is working good so far.
>>>
>>> Cheers,
>>>
>>> -Original Message-
>>> From: gmx-users-boun...@gromacs.org
>>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
>>> Sent: Thursday, 24 March 2011 1:36 PM
>>> To: Gromacs Users' List
>>> Subject: Re: [gmx-users] no output dgdl file
>>>
>>>
>>>
>>> Emanuel Birru wrote:

 Hi Justin,

 It good that the issue is solved. As per my experience if you want to
>>>
>>> do

 a series of simulations it is not necessary to use foreign_lambda, for
 each simulation we can give different lambda values starting from 0 to
 1( from fully interactive to non-interactive) no need of foreign_lamda
>>>
>>> This is certainly a viable method, but it is thermodynamic integration,
>>> not BAR.   The purpose of lambda/foreign_lambda is to use the BAR method.
>>>
 and certainly no need of generating dhdl.xvg to calculate FE. I think
 -dhdl is an optional it will not be generated just because
>>>
>>> "free_energy

 = yes" is present. The problem with the 4.5.3 is not the problem of
>>>
>>> It has always been my experience (in versions 3.3.3 and 4.5.3) that if
>>> the free energy code is activated, this file is written.  I never specify
>>> the
>>> file names independently.
>>>
 generating dhdl data by using single simulation with all
>>>
>>> foreign_lambda

 values. The problem is with g_bar, when I tried to analyse the
>>>
>>> dhdl.xvg

 output (with all the necessary data in it) using g_bar, it do

Re: [gmx-users] no output dgdl file

[Szilárd Páll]

> I am a bit confused on the g_bar part, when it says -f expects multiple
> dhdl files. Do we need to run still multiple independent simulations
> using different foreign_lambda values? I do not see why we should run
> independent simulations, if we use for couple-lambda0 and couple-lambda1
> vdw-q and none respectively.
>

As Justin said, you do need multiple simulations. That is because you
need overlap between state lam_i lam_j to sample and estimate the dG
efficiently . If you only have two states, lambda 0 and 1 you will
most probably have a very poor overlap and therefor a poor dG
estimate.

g_bar expects you to provide a set of dhdl (with -f) or edr (with -e)
files corresponding to you individual simulations at the chosen lambda
values and for every lambda it needs the foreign lambdas provided in
the mdp file.

--
Szilárd


> -Original Message-
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Thursday, 24 March 2011 1:36 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] no output dgdl file
>
>
>
> Emanuel Birru wrote:
>> Hi Justin,
>>
>> It good that the issue is solved. As per my experience if you want to
> do
>> a series of simulations it is not necessary to use foreign_lambda, for
>> each simulation we can give different lambda values starting from 0 to
>> 1( from fully interactive to non-interactive) no need of foreign_lamda
>
> This is certainly a viable method, but it is thermodynamic integration,
> not BAR.
>  The purpose of lambda/foreign_lambda is to use the BAR method.
>
>> and certainly no need of generating dhdl.xvg to calculate FE. I think
>> -dhdl is an optional it will not be generated just because
> "free_energy
>> = yes" is present. The problem with the 4.5.3 is not the problem of
>
> It has always been my experience (in versions 3.3.3 and 4.5.3) that if
> the free
> energy code is activated, this file is written.  I never specify the
> file names
> independently.
>
>> generating dhdl data by using single simulation with all
> foreign_lambda
>> values. The problem is with g_bar, when I tried to analyse the
> dhdl.xvg
>> output (with all the necessary data in it) using g_bar, it doesn't
>> function properly. The error is related with the source code. I guess
>
> If you suspect a bug, you should report it.  If you don't use
> foreign_lambda,
> you can't use the BAR method.  You're doing TI, not BAR.  They are
> fundamentally
> different, and the analysis for TI is done independently of any Gromacs
> tool.
>
>> the main advantage of using 4.5.3 to calculated FE using
> foreign_lambda
>> was to avoid running series of independent simulations. May be it is
>> solved on the newer version 4.5.4., didn't try it yet.
>>
>
> Version 4.5.3 has worked just fine for all free energy calculations I
> have done.
>   Perhaps BAR can be done with a single simulation and multiple
> foreign_lambda,
> but that was not my understanding of the proper procedure (based on some
> posts
> by developers a few months ago).  Multiple simulations, each at "native"
> lambda,
> are conducted with values of foreign_lambda above and below the native
> value at
> some lambda spacing (except for end points).  Invoking g_bar gives the
> total
> DeltaG over all lambda intervals according to the BAR algorithm.
>
> -Justin
>
>> Cheers,
>>
>>
>>
>> -Original Message-
>> From: gmx-users-boun...@gromacs.org
>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
>> Sent: Thursday, 24 March 2011 12:54 PM
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] no output dgdl file
>>
>>
>>
>> Emanuel Birru wrote:
>>> Hi Justin,
>>>
>>> Sure what you wrote is correct, what I am trying to tell to him is
>> that
>>> if he has more than one foreign lambda it is better to put all of
> them
>>> as it is not logical to use only one foreign lambda to calculate FE
> (0
>> -
>>> 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about
>>
>> You can do a series of simulations at many values of lambda, each
>> specifying
>> their own foreign_lambda.  It seems to me that this method would be
> more
>>
>> reliable, but I have not tested simply attempting a single simulation
>> with all
>> values of foreign_lambda.  Using delta_lambda is (from all that I have
>> read) not
>> reliable, as there are known issues with "slow growth" methods.
>>
>>> file names but it also generate all the necessary files including the
>>> xvg's without the need of using -dhdl.
>>>
>>
>> Whether or not one specifies -dhdl or -deffnm is independent of
> whether
>> or not
>> dhdl.xvg (or whatever name) is written.  It is controlled purely by
> the
>> presence
>> of "free_energy = yes" in the input file.
>>
>>> I would appreciate if you come up with a new solution for him.
>>>
>>
>> As reported by the OP, this issue had been effectively solved already:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html
>>
>> -Justin
>>
>>> Cheers
>

[gmx-users] Automated RMSD Calculations

[Nancy]

Hi All,

I would like to calculate RMSDs of a large number of small molecule
conformations against a reference conformation, is there a simple software
program or method that can be used to perform such calculations?

Thanks in advance,
Nancy
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Re: [gmx-users] Automated RMSD Calculations

[Justin A. Lemkul]

Nancy wrote:

Hi All,

I would like to calculate RMSDs of a large number of small molecule 
conformations against a reference conformation, is there a simple 
software program or method that can be used to perform such calculations?


This can easily be scripted:

http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive

-Justin



Thanks in advance,
Nancy




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Automated RMSD Calculations

[Nancy]

Thanks alot for the info.
Nancy


On Fri, Mar 25, 2011 at 6:22 PM, Justin A. Lemkul  wrote:

>
>
> Nancy wrote:
>
>> Hi All,
>>
>> I would like to calculate RMSDs of a large number of small molecule
>> conformations against a reference conformation, is there a simple software
>> program or method that can be used to perform such calculations?
>>
>
> This can easily be scripted:
>
>
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
>
> -Justin
>
>
>> Thanks in advance,
>> Nancy
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[Mark Abraham]

On 26/03/2011 2:27 AM, maria goranovic wrote:
Yes, that would be the correct way to do this. I was hoping to take a 
shorter route, and just modifying a couple of dihedrals in the 
topology files output by pdb2gmx without having to make a new residue. 
Is that not possible at all ?


Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in a 
general sense. It generates a topology that matches given coordinates, 
fixing a few details as directed. It will fill valences with hydrogen 
atoms, generate terminal groups, organize disulfides, and choose 
protonation states of titratable residues, but it won't change 
geometries in the way you seem to want.


Neither does anything in the .top/.itp files stipulate the chirality of 
any center (in all-atom models). Various dihedral angles change sign 
with chirality, but the dihedral functions are all symmetric about the 
y-axis (i.e. even). So I suspect you do not need to change anything 
about the topology. Just use a molecule builder to change the chirality 
of the relevant center in the input file to pdb2gmx.


Mark

On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar > wrote:


Hi Maria,

The general solution is to copy the entry in the .rtp file, modify the
dihedrals involved, and rename the entry to match the name used in the
coordinate (pdb) file. You may also need to copy the entries in the
.hdb file, as well as the .tdb files if it is a terminal residue.

Hope it helps,

Tsjerk

On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic
mailto:mariagorano...@gmail.com>> wrote:
> Hi
> Appreciate the quick help
> I am sorry, this is not an improper, but a proper dihedral that
holds the
> chirality in place. Then the solution suggested by Meli would
not work? I do
> not have a D-ASP. I in fact have an L-ASP which i want to
convert to D. So
> the question is simply how to set the proper chirality to a
D-amino acid in
> CHARMM.
>
>
> Maria
> On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar
mailto:tsje...@gmail.com>>
> wrote:
>>
>> Hi Maria,
>>
>> The CHARMM force field is an all-atom one. That means it does not
>> require improper dihedrals to maintain chirality. If you have a
D-ASP
>> in your structure file, you can rename it to ASP and just run
pdb2gmx.
>> Mind not to regenerate hydrogens in that case, or make sure to
modify
>> the hydrogen position for the D amino acids afterwards, to set the
>> proper chirality.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
>> mailto:mariagorano...@gmail.com>> wrote:
>> > Hello List
>> > I want to change an ASP to a D-ASP. I think it should be
possible by
>> > simply
>> > changing 2 improper values around the chiral carbon to their
opposite
>> > sign.
>> > Instead of making a brand new residue, I thought I would take the
>> > topology
>> > of an ASP generated by pdb2gmx, and simply change values
manually in the
>> > resulting .itp. However, this is not possible because gromacs
wants to
>> > read
>> > the dihedral parameters from the ffbonded.itp file. Is it
possible for
>> > me to
>> > explicitly state the parameters for these two dihedrals in my
d-asp.itp
>> > file? This will be the fastest solution to the problem because it
>> > precludes
>> > making a new residue or defining new atoms types and so on.
With the
>> > CHARMM
>> > force field, I am not sure how  q0 cq translate to c0 c1 c2
and c3 which
>> > we
>> > are used to for gromos topologies.
>> > The mailing list search function was down, so I could not
explore prior
>> > messages about this.
>> > --
>> > Maria
>> >
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>> > --
>> > gmx-users mailing list gmx-users@gromacs.org

>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org
.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
>> gmx-users mailing list gmx-users@gromacs.org

>> http://lists.gromacs.org/mailm

Re: [gmx-users] g_cluster segmentation fault

[Mark Abraham]

On 26/03/11, Craig Kitchen   wrote:
> Dear All,
> 
> When running g_cluster on a file generated with g_mdmat I receive a 
> segmentation fault. I have tried different versions of Gromacs (4.0.5 and 
> 4.5.3) on different workstations with both large and small matrices - all 
> without success.
> 

Good trouble-shooting and report. You'd likely have been asked to check a 
recent version and with a small matrix :-)

This was a two-part bug - a clean-up function was called when the corresponding 
initialization hadn't been called, and that clean-up function assumed that 
initialization had happened. I fixed both in git.

You can work around this by hacking in src/tools/gmx_cluster.c. Around line 
1260 there will be code like

if (bPBC) {
  gmx_rmpbc_done(gpbc);
}

which you should move one line up (inside a set of braces that mean the 
clean-up is called only after initialization occurs). Don't worry about the 
indenting.

Mark


> I am calling g_cluster with:
> 
> g_cluster -dm dmat_1.xpm -cutoff 3.4 -g cluster_1.log
> 
> Whereupon I receive the error:
> 
> Using linkage method for clustering
> Reading rms distance matrix 100%
> Segmentation fault
> 
> The distance matrix (dmat_1.xpm) was generated with:
> 
> g_mdmat -f onlyba.gro -s onlyba.gro -t 4.0 -mean dmat_1.xpm
> 
> The configuration (onlyba.gro) and matrix file (dmat_1.xpm) are attached (and 
> since they are short also pasted below).
> 
> Any help on this would be greatly appreciated!
> 
> Regards,
> 
> Craig
> 
> Craig Kitchen
> Department of Chemistry
> University of Cambridge
> Lensfield Road
> Cambridge
> CB2 1EW
> UK
> 
> 
> 
> 
> Generated by trjconv : Coarse-Grained Model of EAS Barrels and Loop Residues 
> (including bonds) t= 0.0
>  10
>   1BA  BA    1  44.780  21.592  37.304  0.0067  0.0035  0.0073
>  29BA  BA    2  12.191  38.323   0.704 -0.0084  0.0108 -0.0014
>  57BA  BA    3   2.092   9.298  47.957  0.0053 -0.0144  0.0053
>  85BA  BA    4  15.664  33.182  25.406  0.0291 -0.0067 -0.0069
> 113BA  BA    5  47.194  32.613  24.031 -0.0146 -0.0132  0.0184
> 141BA  BA    6  11.731  25.247  11.921 -0.0100 -0.0049  0.0025
> 169BA  BA    7  33.751  20.349  25.599 -0.0103 -0.0131  0.0078
> 197BA  BA    8   2.467  11.277  47.988 -0.0063  0.0188 -0.0001
> 225BA  BA    9  25.948  26.283  35.007  0.0191  0.0058  0.0047
> 253BA  BA   10  26.103  27.621  36.697 -0.0057  0.0281 -0.0110
> 48.0  48.0  48.0
> 
> 
> /* XPM */
> /* Generated by g_mdmat */
> /* This file can be converted to EPS by the GROMACS program xpm2ps */
> /* title:   "Mean smallest distance" */
> /* legend:  "Distance (nm)" */
> /* x-label: "Residue Index" */
> /* y-label: "Residue Index" */
> /* type:    "Continuous" */
> static char *gromacs_xpm[] = {
> "10 10   40 1",
> "A  c #FF " /* "0" */,
> "B  c #F8F8F8 " /* "0.103" */,
> "C  c #F2F2F2 " /* "0.205" */,
> "D  c #EBEBEB " /* "0.308" */,
> "E  c #E5E5E5 " /* "0.41" */,
> "F  c #DEDEDE " /* "0.513" */,
> "G  c #D8D8D8 " /* "0.615" */,
> "H  c #D1D1D1 " /* "0.718" */,
> "I  c #CBCBCB " /* "0.821" */,
> "J  c #C4C4C4 " /* "0.923" */,
> "K  c #BEBEBE " /* "1.03" */,
> "L  c #B7B7B7 " /* "1.13" */,
> "M  c #B1B1B1 " /* "1.23" */,
> "N  c #AA " /* "1.33" */,
> "O  c #A3A3A3 " /* "1.44" */,
> "P  c #9D9D9D " /* "1.54" */,
> "Q  c #969696 " /* "1.64" */,
> "R  c #909090 " /* "1.74" */,
> "S  c #898989 " /* "1.85" */,
> "T  c #838383 " /* "1.95" */,
> "U  c #7C7C7C " /* "2.05" */,
> "V  c #767676 " /* "2.15" */,
> "W  c #6F6F6F " /* "2.26" */,
> "X  c #696969 " /* "2.36" */,
> "Y  c #626262 " /* "2.46" */,
> "Z  c #5C5C5C " /* "2.56" */,
> "a  c #55 " /* "2.67" */,
> "b  c #4E4E4E " /* "2.77" */,
> "c  c #484848 " /* "2.87" */,
> "d  c #414141 " /* "2.97" */,
> "e  c #3B3B3B " /* "3.08" */,
> "f  c #343434 " /* "3.18" */,
> "g  c #2E2E2E " /* "3.28" */,
> "h  c #272727 " /* "3.38" */,
> "i  c #212121 " /* "3.49" */,
> "j  c #1A1A1A " /* "3.59" */,
> "k  c #141414 " /* "3.69" */,
> "l  c #0D0D0D " /* "3.79" */,
> "m  c #070707 " /* "3.9" */,
> "n  c #00 " /* "4" */,
> /* x-axis:  1 2 3 4 5 6 7 8 9 10 */
> /* y-axis:  1 2 3 4 5 6 7 8 9 10 */
> "VA",
> "AV",
> "nnUAnn",
> "nnAnnn",
> "nA",
> "An",
> "nnnAnn",
> "nnAUnn",
> "nA",
> "An"
>
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