Re: Re: [gmx-users] Nose-hoover T-coupling in REMD

[wibke . sudholt]

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Re: [gmx-users] Nose-hoover T-coupling in REMD

[Qin Qiao]

2010/12/26 ms 

> On 25/12/10 02:12, Qin Qiao wrote:
>>>
>>>  Thanks a lot!

 It says Nose-hoover coupling generates the correct canonical ensemble,
 and
 that's the reason why I used it. I wonder whether v-rescale can also get
 the
 correct ensemble. Could you tell me?


>>> As far as I know v-rescale should generate a correct ensemble.
>>>
>>
> On 25/12/10 12:40, Qin Qiao wrote:
> > I'm not sure, since actually kinetic energy should have fluctuation, and
> the
> > v-rescaling may suppress the fluctuation..
> >
>
> (PLEASE don't top post!!)
>
> Well, the thermostat author, who I happen to know, says it generates the
> right ensemble. :) I'm not an expert so I can't say if it's true, but if you
> like you can read the original papers, linked here:
>
>
> http://sites.google.com/site/giovannibussi/Research/algorithms#TOC-A-stochastic-velocity-rescaling-the
>
> cheers,
>
> m.
>
> Thanks a lot!

Qin

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[gmx-users] Atomype HW not found

[trevor brown]

Dear all,
I have "Atomype HW not found" error when I use gromos43a1 in water at the
end of grompp.
However there is no error if I just change the forcefield to oplsaa.
My topology file follows.

Any suggestions?

trevor

; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   4 CYS rtp CYS2 q +1.0
 1 NL  4CYS  N  1  0.12914.0067   ; qtot
0.129
 2  H  4CYS H1  1  0.248  1.008   ; qtot
0.377
 3  H  4CYS H2  1  0.248  1.008   ; qtot
0.625
 4  H  4CYS H3  1  0.248  1.008   ; qtot
0.873
 5CH1  4CYS CA  2  0.127 13.019   ; qtot
1
 6CH2  4CYS CB  2  0 14.027   ; qtot
1
 7  S  4CYS SG  2  0  32.06   ; qtot
1
 8  C  4CYS  C  3   0.38 12.011   ; qtot
1.38
 9  O  4CYS  O  3  -0.3815.9994   ; qtot
1
; residue   5 ILE rtp ILE  q  0.0
10  N  5ILE  N  4  -0.2814.0067   ; qtot
0.72
11  H  5ILE  H  4   0.28  1.008   ; qtot
1

.
.
.
.
..
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "gromos43a1.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
OMEGA-AGA-IVB in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
SOL  3177
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Re: [gmx-users] To make continuous trj in REMD

[Qin Qiao]

2011/1/7 Justin A. Lemkul 
>
>
> Qin Qiao wrote:
>>
>>
>> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>    Qin Qiao wrote:
>>
>>
>>
>>        2011/1/7 Justin A. Lemkul >         >        >>
>>
>>
>>
>>
>>           Qin Qiao wrote:
>>
>>               Dear all,
>>
>>               I came across a problem when I want to make the REMD
>>               trajectories continuous.
>>
>>               What I did:
>>
>>               1. 'demux.pl  
>>         REMD_0.log'                 --to get the
>>        'replica_index.xvg'
>>
>>
>>               2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux
>>               ../replica_index.xvg'
>>
>>               It seems smooth. But when I check the rmsd of the output
>>               0_resort.xtc, I found it's still discontinuous.. with big
>>        jumps
>>               about 0.5nm..! Could you help me to figure out what's wrong?
>>               Thanks a lot.
>>
It has been solved. The reason is for the order of the xtc file in
trjcat.  I should use  -f ../REMD_?.xtc ../REMD_??.xtc to get the
correct order, or it will be mixed. Many thanks to Prof. Spoel!
>>
>>           Have you properly accounted for periodicity effects?
>>
>>           -Justin
>>
>>
>>        It's the same after I remove periodicity by trjconv -pbc mol -ur
>>        compact ...
>>
>>
>>    One iteration of trjconv is not necessarily enough to produce a
>>    properly imaged trajectory.  What is going on in the trajectory when
>>    these spikes are occurring?
>>
>>    -Justin
>>
>> In VMD, it just seems to change to a different conformation...
>>
>
> Then it sounds like something has gone wrong with the demultiplexing.  As for 
> what that is, it's hard to say.  Look into the .log file and resulting .xvg 
> file (from demux.pl) to make sure that the proper exchanges were identified.  
> Then try to determine from which replica that sudden change arose (i.e., in 
> which of the original trajectories was that configuration present).  Finding 
> it should be relatively easy; just dump out the frames at that time point 
> from each of the trajectories to see.
>
> For further troubleshooting, it would also be useful to know your Gromacs 
> version, in case there is some sort of bug.  It is too early to tell, though, 
> where the problem lies.
>
> -Justin
>
>>               Best,
>>
>>               Qin
>>
>>           --     
>>
>>           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 list    gmx-us...@gromacs.org
>>        
>>           >
>>
>>           http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>           interface or send it to gmx-users-requ...@gromacs.org
>>        
>>           >        >.
>>
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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
>>
>>    
>>    --     gmx-users mailing list    gmx-us...@gromacs.org
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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
>
> ===

[gmx-users] Atomtpe HW not found-2

[trevor brown]

Dear friends,
My run commands are below. It works without any error.
However if I add -water tip3p at the end of pdg2gmx ... line it causes an
error (Atomtpe HW not found) at grompp time.

Could anyone explain the difference?

trevor

pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top
editconf -f fws.gro -bt dodecahedron -d 1.0
editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2
genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top
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Re: [gmx-users] Atomtpe HW not found-2

[Mark Abraham]

On 10/01/2011 2:41 AM, trevor brown wrote:

Dear friends,
My run commands are below. It works without any error.
However if I add -water tip3p at the end of pdg2gmx ... line it causes 
an error (Atomtpe HW not found) at grompp time.

Could anyone explain the difference?
trevor
pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top
editconf -f fws.gro -bt dodecahedron -d 1.0
editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2
genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top


Not all water models are intended to go with all force fields. G43a1 
does not define the HW atom type used for TIP3P water, possibly by 
Berk's design :-). I don't remember whether it's reasonable to want to 
use TIP3P with the GROMOS forcefields, but presumably SPC water will 
work with them.


Mark
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[gmx-users] Pioglitazone Tautomers

[Nancy]

Hi All,

I am performing molecular docking and molecular dynamics simulations of the
thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein
(PDB ID: 1ZGY).  The thiazolidinedione ring can exist in numerous different
tautomeric states; I have attached a figure depicting several of them.
Which tautomer would be dominant at the physiological pH of ~7.0?

Also, are there any software programs that can predict which tautomer would
be correct?

Thanks in advance,
Nancy
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Re: [gmx-users] Pioglitazone Tautomers

[wibke . sudholt]

Dear Email Sender,

Thank you very much for contacting me! Unfortunately, I am not available in the 
office at the moment and cannot respond to your email. I will be able to handle 
your request starting again Monday, January 10, 2011.

For all questions about CloudBroker, please contact the company under 
i...@cloudbroker.com. In case you have any issues with the CloudBroker 
Platform, please send an email to our helpdesk at platf...@cloudbroker.com. If 
you need to talk to me in person for urgent or important issues, please call my 
mobile phone number.

Kind regards,

Wibke Sudholt


-- 
Dr. Wibke Sudholt
Associate and Chair of the Management
CloudBroker GmbH
Technoparkstrasse 1
CH-8005 Zurich
Switzerland
Phone: +41 44 633 79 34
Email:  i...@cloudbroker.com
Web:http://www.cloudbroker.com



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RE: [gmx-users] Pioglitazone Tautomers

[Dallas Warren]

If you have the pKa for each of those three groups, then you can
calculate that yourself very quickly.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Nancy
Sent: Monday, 10 January 2011 10:12 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Pioglitazone Tautomers

 

Hi All,

I am performing molecular docking and molecular dynamics simulations of
the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor
protein (PDB ID: 1ZGY).  The thiazolidinedione ring can exist in
numerous different tautomeric states; I have attached a figure depicting
several of them.  Which tautomer would be dominant at the physiological
pH of ~7.0?

Also, are there any software programs that can predict which tautomer
would be correct?

Thanks in advance,
Nancy



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Re: [gmx-users] Pioglitazone Tautomers

[Mark Abraham]

On 10/01/2011 10:11 AM, Nancy wrote:

Hi All,

I am performing molecular docking and molecular dynamics simulations 
of the thiazolidinedione pioglitazone binding to the PPAR-gamma 
receptor protein (PDB ID: 1ZGY).  The thiazolidinedione ring can exist 
in numerous different tautomeric states; I have attached a figure 
depicting several of them.  Which tautomer would be dominant at the 
physiological pH of ~7.0?


Also, are there any software programs that can predict which tautomer 
would be correct?


Googling "tautomer prediction" looks like it has good leads.

Mark
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[gmx-users] Water models usage info

[trevor brown]

Dear Mark,
Thank you for your reply which solved my problem.
I want to add something for all gmx-users. I looked at the force field
folders in share/top in which possible usable water models for each force
field are listed in watermodels.dat files. If you want to use a different
model that is not included in the list, look at the "pdb2gmx" title
at the end of the manual.

trevor


On 10/01/2011 2:41 AM, trevor brown wrote:
> Dear friends,
> My run commands are below. It works without any error.
> However if I add -water tip3p at the end of pdg2gmx ... line it causes
> an error (Atomtpe HW not found) at grompp time.
> Could anyone explain the difference?
> trevor
> pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top
> editconf -f fws.gro -bt dodecahedron -d 1.0
> editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2
> genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top

Not all water models are intended to go with all force fields. G43a1
does not define the HW atom type used for TIP3P water, possibly by
Berk's design :-). I don't remember whether it's reasonable to want to
use TIP3P with the GROMOS forcefields, but presumably SPC water will
work with them.

Mark
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Re: [gmx-users] Pioglitazone Tautomers

[Tsjerk Wassenaar]

Hi Nancy,

This isn't really a Gromacs related question, and it would be better
fit on some chemistry forum. Anyway, whatever answer may come to you,
mind that you're interested in the receptor bound form, which may not
be what you'll find to be the dominant form. It will depend on the
hydrogen bonded network in the pocket. Also, the proton is also
probably quite acidic, as the negative charge can delocalize nicely
over the ring and the carbonyls, so make sure you're looking at the
protonation state too.

Hope it helps,

Tsjerk

On Mon, Jan 10, 2011 at 12:11 AM, Nancy  wrote:
> Hi All,
>
> I am performing molecular docking and molecular dynamics simulations of the
> thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein
> (PDB ID: 1ZGY).  The thiazolidinedione ring can exist in numerous different
> tautomeric states; I have attached a figure depicting several of them.
> Which tautomer would be dominant at the physiological pH of ~7.0?
>
> Also, are there any software programs that can predict which tautomer would
> be correct?
>
> Thanks in advance,
> Nancy
>
>
>
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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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