[gmx-users] Speeding things up

2009-08-14 Thread Borys Szefczyk 
Dear Gromacs Users,

I am was wondering if I would be able tweak my simulation to run it
a bit faster. According to the chapter 3.17 of the manual, I have setup
the cut-offs and Fourier grid spacing so that the PME load is around 25%.
However, Gromacs still complains in the log file about the performance
loss due to the load imballance:

D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 49748.7
 av. #atoms communicated per step for LINCS:  2 x 4755.5

 Average load imbalance: 29.1 %
 Part of the total run time spent waiting due to load imbalance: 17.1 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %

NOTE: 17.1 % performance was lost due to load imbalance
  in the domain decomposition.


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp. 8   5001  418.999  167.6 0.4
 Comm. coord.   8  50001  312.233  124.9 0.3
 Neighbor search8   500111297.211 4518.712.0
 Force  8  5000155518.68622206.458.7
 Wait + Comm. F 8  50001  761.632  304.6 0.8
 PME mesh   8  5000124141.436 9656.125.5
 Write traj.81053.9901.6 0.0
 Update 8  50001  407.860  163.1 0.4
 Constraints8  50001 1229.791  491.9 1.3
 Comm. energies 8  50001  230.156   92.1 0.2
 Rest   8 182.584   73.0 0.2
---
 Total  8   94504.57837800.0   100.0

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:   4725.000   4725.000100.0
   1h18:45

Is there something I could do about it? I should probably mention
that my system is composed of a slab of molecules and a protein on top
of it, in a cubic box, so there is a lot of vacuum around. I understand
that Gromacs should take care to optimize the domain decomposition
(I use the default parameters for DD). The job is running on 8 cores
of a single machine.

I would appreciate suggestions,
Borys Szefczyk

-- 
 REQUIMTE,  &  Molecular Modelling & Quantum Chemistry Group,
  Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
   Faculty of Science,  &  Wroclaw University of Technology
   University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk
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RE: [gmx-users] Speeding things up

2009-08-14 Thread Berk Hess 

Hi,

For systems with vacuum the automatic domain decomposition setup does
not do a good job. It currently decomposes based on the box dimensions,
not on the actual atom distribution in the box.
I was thinking of improving this a bit for 4.1.

I would guess -dd 4 2 1 will give the best performance.

Berk

> Date: Fri, 14 Aug 2009 10:36:50 +0200
> From: szefc...@mml.ch.pwr.wroc.pl
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Speeding things up
> 
> Dear Gromacs Users,
> 
> I am was wondering if I would be able tweak my simulation to run it
> a bit faster. According to the chapter 3.17 of the manual, I have setup
> the cut-offs and Fourier grid spacing so that the PME load is around 25%.
> However, Gromacs still complains in the log file about the performance
> loss due to the load imballance:
> 
> D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
> 
>  av. #atoms communicated per step for force:  2 x 49748.7
>  av. #atoms communicated per step for LINCS:  2 x 4755.5
> 
>  Average load imbalance: 29.1 %
>  Part of the total run time spent waiting due to load imbalance: 17.1 %
>  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %
> 
> NOTE: 17.1 % performance was lost due to load imbalance
>   in the domain decomposition.
> 
> 
>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> 
>  Computing: Nodes Number G-CyclesSeconds %
> ---
>  Domain decomp. 8   5001  418.999  167.6 0.4
>  Comm. coord.   8  50001  312.233  124.9 0.3
>  Neighbor search8   500111297.211 4518.712.0
>  Force  8  5000155518.68622206.458.7
>  Wait + Comm. F 8  50001  761.632  304.6 0.8
>  PME mesh   8  5000124141.436 9656.125.5
>  Write traj.81053.9901.6 0.0
>  Update 8  50001  407.860  163.1 0.4
>  Constraints8  50001 1229.791  491.9 1.3
>  Comm. energies 8  50001  230.156   92.1 0.2
>  Rest   8 182.584   73.0 0.2
> ---
>  Total  8   94504.57837800.0   100.0
> 
> Parallel run - timing based on wallclock.
> 
>NODE (s)   Real (s)  (%)
>Time:   4725.000   4725.000100.0
>1h18:45
> 
> Is there something I could do about it? I should probably mention
> that my system is composed of a slab of molecules and a protein on top
> of it, in a cubic box, so there is a lot of vacuum around. I understand
> that Gromacs should take care to optimize the domain decomposition
> (I use the default parameters for DD). The job is running on 8 cores
> of a single machine.
> 
> I would appreciate suggestions,
> Borys Szefczyk
> 
> -- 
>  REQUIMTE,  &  Molecular Modelling & Quantum Chemistry Group,
>   Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
>Faculty of Science,  &  Wroclaw University of Technology
>University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk
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Re: [gmx-users] Speeding things up

2009-08-14 Thread Borys Szefczyk 
On Fri, Aug 14, 2009 at 10:50:29AM +0200, Berk Hess wrote:
> 
> Hi,
> 
> For systems with vacuum the automatic domain decomposition setup does
> not do a good job. It currently decomposes based on the box dimensions,
> not on the actual atom distribution in the box.
> I was thinking of improving this a bit for 4.1.
> 
> I would guess -dd 4 2 1 will give the best performance.
> 
> Berk

Thanks, the performance is better indeed. The run time is reduced by 12%
comparing to the default partitioning (8x1x1).

Borys

-- 
 REQUIMTE,  &  Molecular Modelling & Quantum Chemistry Group,
  Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
   Faculty of Science,  &  Wroclaw University of Technology
   University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk
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Re: [gmx-users] Exotic metal species

2009-08-14 Thread David van der Spoel 

Lili Peng wrote:

Hi David,

Thanks for your comments.  There is a group that has developed force 
field parameters for the Indium(III)-DTPA using Amber: 
http://www.ncbi.nlm.nih.gov/pubmed/11559086 .  Since the authors were 
able to successfully determine force field parameters for Amber, a 
molecular dynamics package, can I safely assume that charge transfer is 
not an issue for running simulations on In(III)-DTPA using another 
MD-based package like Gromacs?


No you can not assume that. I have not read the paper an am not familiar 
with the system, but you need to be cautious when using this kind of 
model. If you use the Amber force field with these parameters you can of 
course cite this paper and probably get away with it, but be aware of 
the intrinsic problems with these system.


Thanks,
Lili

2009/8/12 David van der Spoel >


Lili Peng wrote:

Der all,

I'd like to know if any has had experience in using GROMACS for
modeling exotic metal species like Gadolinium(III) and
Indium(III)?  My system is actually an Indium(III) ion coupled
to  DTPA (diethylenetriaminepentaacetate), an octadentate ligand
forms bonds with metals through three atoms of nitrogen and five
atoms of oxygen.  I've consulted the Gromacs wiki
(http://www.gromacs.org/WIKI-import/Exotic_Species) and it
suggests that I consult someone with expertise in this area.
 Has anyone had any (successful?) experience in this effort?

It depends on what the ion does, if it only has a structural role,
and is not exposed to solvent, you can model it as any 3+ charge
site, and use covalent bonds or distance restraint to keep it in
place. However, if the ligands are supposed to move away from the
ion it becomes complicated. In any such interaction charge transfer
is significant, but difficult to quantify, and very difficult to
model with clasical models (and with QM models for such a big guy).

Thanks,
Lili




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-- 
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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[gmx-users] preferred/best force fields

2009-08-14 Thread iulek 

Dear All,

I am new to molecular dynamics, had some tutorials and could run  
some initial tests successfully in that they finished without errors  
(now to analyze if results make sense).
Now my challenge is to make a molecular dynamics of a homohexamer  
which binds to a ssDNS and a co-factor, and that looses some of its  
binding capacities when a mutation is present. I could build an  
(non-hydrogen) homology model for the system, but I am still facing  
some problem on conventions for atom names. I could not overcome  
everything still, though.
But in this post I would like to discuss about the best force  
fields to use in the main problems I should face: a) a protein monomer  
in water; b) a protein oligomer in water; c) a protein bound to an  
inhibitor (small organic molecule) in water; d) a protein homohexamer  
bound to DNA and co-factor in water.
I spent the last days gathering some information through the web  
and the gromacs manual. I could learn a lot, but I feel I still miss  
some organization of my understanding. It seems to me that specially  
for case "d" (the very one of the moment) an amber force field port  
(which best, 99SB?) to gromacs should be the preferred one, right?  
Anyway, I would like to make the question wider and ask if someone  
might point me to an article/links/whatever, for the to mature this  
overview, id est, to a compilation of the preferred (or best) force  
field for some typical biochemical MD simulations.

Thanks in advance,

Jorge

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Re: [gmx-users] bad bond in polymer

2009-08-14 Thread nicegromacs 
I follow some of the step of 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I 
omitted the change in the .hdb file because I don't have explicit 
hydrogens). Well, I build a polymer with 3 units. The head (H), one repeat 
unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, but when I 
add one more repetitive unit (H-R-R-T) I get the following error:

Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper

---

"Stop Drinking My Beer !" (The Amps)





nicegromacs wrote:


  CAG -CAM


Defining a bond to a previous residue will certainly fail for at least one 
terminus of your polymer chain.  You may find this post useful:


http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

If things still aren't working, please post the structure file, as well, 
and identify the bond that is being formed that shouldn't.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] bad bond in polymer

2009-08-14 Thread Justin A. Lemkul 



nicegromacs wrote:
I follow some of the step of 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I 
omitted the change in the .hdb file because I don't have explicit 
hydrogens). Well, I build a polymer with 3 units. The head (H), one 
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, 
but when I add one more repetitive unit (H-R-R-T) I get the following 
error:

Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper

---



It looks like pdb2gmx is finding some kind of undefined residue.  Can you post 
the .pdb file?


-Justin


"Stop Drinking My Beer !" (The Amps)





nicegromacs wrote:


  CAG -CAM


Defining a bond to a previous residue will certainly fail for at least 
one terminus of your polymer chain.  You may find this post useful:


http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

If things still aren't working, please post the structure file, as 
well, and identify the bond that is being formed that shouldn't.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Adding a residue

2009-08-14 Thread Smith, Chanel Chonda 
Could anyone give me the proper procedure for adding a residue?  (Using itp)



From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Thu 8/13/2009 1:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Adding a residue





Smith, Chanel Chonda wrote:
> Hello,
> I am currently using GROMACS 4.  When trying to process the pdb file
> with pdb2gmx, an error message came up stating that a particular residue
was
> not recognized by the residue topology database.  I then tried to adding a
> molecule in the ffrtp file and adding the name in aminoacids.dat.  This
> did not work either.  The residue that I need to add is a nonprotein.
Could
> you tell me how I can add this residue to the database and therefore
allowing
> me to process the pdb file?
>

You've followed the correct procedure.  If the new residue is a ligand of
some
sort, it may just be easier to create an .itp file for it (using one of the
user-contributed programs, or something like PRODRG).

If you still want to use the .rtp approach, provide more details, like the
actual .rtp entry and the exact error message that you're getting from
pdb2gmx.

-Justin

>
> Thanks,
> Chanel King
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Adding a residue

2009-08-14 Thread Justin A. Lemkul 



Smith, Chanel Chonda wrote:

Could anyone give me the proper procedure for adding a residue?  (Using itp)



http://oldwiki.gromacs.org/index.php/Tutorials#General

See the drug-enzyme tutorial, but be advised that PRODRG topologies often 
contain unsatisfactory charges and charge groups, requiring manual modification 
and validation (as with any method of deriving parameters, really).


-Justin




From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Thu 8/13/2009 1:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Adding a residue





Smith, Chanel Chonda wrote:

Hello,
I am currently using GROMACS 4.  When trying to process the pdb file
with pdb2gmx, an error message came up stating that a particular residue

was

not recognized by the residue topology database.  I then tried to adding a
molecule in the ffrtp file and adding the name in aminoacids.dat.  This
did not work either.  The residue that I need to add is a nonprotein.

Could

you tell me how I can add this residue to the database and therefore

allowing

me to process the pdb file?



You've followed the correct procedure.  If the new residue is a ligand of
some
sort, it may just be easier to create an .itp file for it (using one of the
user-contributed programs, or something like PRODRG).

If you still want to use the .rtp approach, provide more details, like the
actual .rtp entry and the exact error message that you're getting from
pdb2gmx.

-Justin


Thanks,
Chanel King
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] bad bond in polymer

2009-08-14 Thread nicegromacs 

Hi Justin,

the pdb file:

HETATM1  CAA DRG 1  83.043  46.127  36.820
HETATM2  CAB DRG 1  82.411  45.765  35.421
HETATM3  CAC DRG 1  81.495  46.822  34.598
HETATM4  CAD DRG 1  80.621  46.369  33.071
HETATM5  CAE DRG 1  79.305  47.302  32.172
HETATM6  CAF DRG 1  77.939  46.749  31.124
HETATM7  CAG DRG 1  76.264  47.439  30.612
HETATM8  CAH DRG 1  74.636  46.805  29.962
HETATM9  CAI DRG 1  72.805  47.674  30.179
HETATM   10  CAJ DRG 1  73.794  48.838  31.123
HETATM   11  OAK DRG 1  74.815  49.342  30.292
HETATM   12  OAL DRG 1  74.592  48.143  32.194
HETATM   13  CAM DRG 1  71.093  47.685  29.486
HETATM   14  CAN DRG 1  71.598  47.212  28.208
HETATM   15  OAO DRG 1  72.440  48.255  27.735
HETATM   16  OAP DRG 1  72.374  46.050  28.399
HETATM   17  CAA DRG 1  72.093  46.197  36.714
HETATM   18  CAB DRG 1  71.418  45.759  35.400
HETATM   19  CAC DRG 1  71.084  46.901  34.417
HETATM   20  CAD DRG 1  70.620  46.251  33.139
HETATM   21  CAE DRG 1  70.650  47.255  32.000
HETATM   22  CAF DRG 1  69.655  46.512  30.955
HETATM   23  CAG DRG 1  69.081  47.504  29.843
HETATM   24  CAH DRG 1  67.208  47.518  29.256
HETATM   25  CAI DRG 1  65.298  47.601  29.691
HETATM   26  CAJ DRG 1  65.629  48.362  30.827
HETATM   27  OAK DRG 1  65.140  49.590  30.429
HETATM   28  OAL DRG 1  64.837  47.815  31.709
HETATM   29  CAM DRG 1  63.041  47.557  29.333
HETATM   30  CAN DRG 1  62.808  47.023  27.931
HETATM   31  OAO DRG 1  63.130  48.142  27.185
HETATM   32  OAP DRG 1  63.560  45.894  27.706
HETATM   33  CAA DRG 1  61.174  46.188  36.668
HETATM   34  CAB DRG 1  60.510  45.777  35.344
HETATM   35  CAC DRG 1  60.221  46.928  34.352
HETATM   36  CAD DRG 1  59.724  46.337  32.998
HETATM   37  CAE DRG 1  60.252  47.307  31.985
HETATM   38  CAF DRG 1  61.089  46.606  30.881
HETATM   39  CAG DRG 1  60.868  47.564  29.740
HETATM   40  CAH DRG 1  58.621  47.652  29.253
HETATM   41  CAI DRG 1  56.328  47.703  29.755
HETATM   42  CAJ DRG 1  55.914  48.516  30.963
HETATM   43  OAK DRG 1  55.050  49.545  30.403
HETATM   44  OAL DRG 1  54.945  47.724  31.565
HETATM   45  CAM DRG 1  54.420  47.478  29.367
HETATM   46  CAN DRG 1  53.587  47.142  27.983
HETATM   47  OAO DRG 1  52.713  48.009  27.325
HETATM   48  OAP DRG 1  53.396  45.805  27.517
HETATM   49  CAA DRG 1  50.257  46.173  36.646
HETATM   50  CAB DRG 1  49.673  45.778  35.270
HETATM   51  CAC DRG 1  49.360  46.939  34.273
HETATM   52  CAD DRG 1  49.270  46.480  32.735
HETATM   53  CAE DRG 1  50.289  47.086  31.602
HETATM   54  CAF DRG 1  51.813  46.713  31.234
HETATM   55  CAG DRG 1  52.487  47.720  29.966
HETATM   56  CAH DRG 1  50.870  47.989  29.178
HETATM   57  CAI DRG 1  48.982  47.816  29.191
HETATM   58  CAJ DRG 1  47.901  48.319  30.192
HETATM   59  OAK DRG 1  47.004  49.132  29.503
HETATM   60  OAL DRG 1  46.963  47.171  30.588
HETATM   61  CAM DRG 1  47.752  46.922  28.157
HETATM   62  CAN DRG 1  46.372  47.149  27.020
HETATM   63  OAO DRG 1  45.018  47.950  26.877
HETATM   64  OAP DRG 1  46.019  46.082  26.137


--
From: "Justin A. Lemkul" 
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" 
Subject: Re: [gmx-users] bad bond in polymer




nicegromacs wrote:
I follow some of the step of 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I 
omitted the change in the .hdb file because I don't have explicit 
hydrogens). Well, I build a polymer with 3 units. The head (H), one 
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, 
but when I add one more repetitive unit (H-R-R-T) I get the following 
error:

Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper

---



It looks like pdb2gmx is finding some kind of undefined residue.  Can you 
post the .pdb file?


-Justin


"Stop Drinking My Beer !" (The Amps)





nicegromacs wrote:


  CAG -CAM


Defining a bond to a previous residue will certainly fail for at least 
one terminus of your polymer chain.  You may find this post useful:


http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

If things still aren't working, please post the structure file, as well, 
and identify the bond that is being formed that shouldn't.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTA

Re: [gmx-users] bad bond in polymer

2009-08-14 Thread Justin A. Lemkul 


All of your residue numbers are one, so I think pdb2gmx is trying to make them 
all one residue.  Try giving each unit a sequential residue number.


-Justin

nicegromacs wrote:

Hi Justin,

the pdb file:

HETATM1  CAA DRG 1  83.043  46.127  36.820
HETATM2  CAB DRG 1  82.411  45.765  35.421
HETATM3  CAC DRG 1  81.495  46.822  34.598
HETATM4  CAD DRG 1  80.621  46.369  33.071
HETATM5  CAE DRG 1  79.305  47.302  32.172
HETATM6  CAF DRG 1  77.939  46.749  31.124
HETATM7  CAG DRG 1  76.264  47.439  30.612
HETATM8  CAH DRG 1  74.636  46.805  29.962
HETATM9  CAI DRG 1  72.805  47.674  30.179
HETATM   10  CAJ DRG 1  73.794  48.838  31.123
HETATM   11  OAK DRG 1  74.815  49.342  30.292
HETATM   12  OAL DRG 1  74.592  48.143  32.194
HETATM   13  CAM DRG 1  71.093  47.685  29.486
HETATM   14  CAN DRG 1  71.598  47.212  28.208
HETATM   15  OAO DRG 1  72.440  48.255  27.735
HETATM   16  OAP DRG 1  72.374  46.050  28.399
HETATM   17  CAA DRG 1  72.093  46.197  36.714
HETATM   18  CAB DRG 1  71.418  45.759  35.400
HETATM   19  CAC DRG 1  71.084  46.901  34.417
HETATM   20  CAD DRG 1  70.620  46.251  33.139
HETATM   21  CAE DRG 1  70.650  47.255  32.000
HETATM   22  CAF DRG 1  69.655  46.512  30.955
HETATM   23  CAG DRG 1  69.081  47.504  29.843
HETATM   24  CAH DRG 1  67.208  47.518  29.256
HETATM   25  CAI DRG 1  65.298  47.601  29.691
HETATM   26  CAJ DRG 1  65.629  48.362  30.827
HETATM   27  OAK DRG 1  65.140  49.590  30.429
HETATM   28  OAL DRG 1  64.837  47.815  31.709
HETATM   29  CAM DRG 1  63.041  47.557  29.333
HETATM   30  CAN DRG 1  62.808  47.023  27.931
HETATM   31  OAO DRG 1  63.130  48.142  27.185
HETATM   32  OAP DRG 1  63.560  45.894  27.706
HETATM   33  CAA DRG 1  61.174  46.188  36.668
HETATM   34  CAB DRG 1  60.510  45.777  35.344
HETATM   35  CAC DRG 1  60.221  46.928  34.352
HETATM   36  CAD DRG 1  59.724  46.337  32.998
HETATM   37  CAE DRG 1  60.252  47.307  31.985
HETATM   38  CAF DRG 1  61.089  46.606  30.881
HETATM   39  CAG DRG 1  60.868  47.564  29.740
HETATM   40  CAH DRG 1  58.621  47.652  29.253
HETATM   41  CAI DRG 1  56.328  47.703  29.755
HETATM   42  CAJ DRG 1  55.914  48.516  30.963
HETATM   43  OAK DRG 1  55.050  49.545  30.403
HETATM   44  OAL DRG 1  54.945  47.724  31.565
HETATM   45  CAM DRG 1  54.420  47.478  29.367
HETATM   46  CAN DRG 1  53.587  47.142  27.983
HETATM   47  OAO DRG 1  52.713  48.009  27.325
HETATM   48  OAP DRG 1  53.396  45.805  27.517
HETATM   49  CAA DRG 1  50.257  46.173  36.646
HETATM   50  CAB DRG 1  49.673  45.778  35.270
HETATM   51  CAC DRG 1  49.360  46.939  34.273
HETATM   52  CAD DRG 1  49.270  46.480  32.735
HETATM   53  CAE DRG 1  50.289  47.086  31.602
HETATM   54  CAF DRG 1  51.813  46.713  31.234
HETATM   55  CAG DRG 1  52.487  47.720  29.966
HETATM   56  CAH DRG 1  50.870  47.989  29.178
HETATM   57  CAI DRG 1  48.982  47.816  29.191
HETATM   58  CAJ DRG 1  47.901  48.319  30.192
HETATM   59  OAK DRG 1  47.004  49.132  29.503
HETATM   60  OAL DRG 1  46.963  47.171  30.588
HETATM   61  CAM DRG 1  47.752  46.922  28.157
HETATM   62  CAN DRG 1  46.372  47.149  27.020
HETATM   63  OAO DRG 1  45.018  47.950  26.877
HETATM   64  OAP DRG 1  46.019  46.082  26.137


--
From: "Justin A. Lemkul" 
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" 
Subject: Re: [gmx-users] bad bond in polymer




nicegromacs wrote:
I follow some of the step of 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html 
(I omitted the change in the .hdb file because I don't have explicit 
hydrogens). Well, I build a polymer with 3 units. The head (H), one 
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives 
ok, but when I add one more repetitive unit (H-R-R-T) I get the 
following error:

Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper

---



It looks like pdb2gmx is finding some kind of undefined residue.  Can 
you post the .pdb file?


-Justin


"Stop Drinking My Beer !" (The Amps)





nicegromacs wrote:


  CAG -CAM


Defining a bond to a previous residue will certainly fail for at 
least one terminus of your polymer chain.  You may find this post 
useful:


http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

If things still aren't working, please post t

Re: [gmx-users] bad bond in polymer

2009-08-14 Thread nicegromacs 

Hi Justin,

ups!! I am sorry this is the exact .pdb file.

HETATM1  CAA DR0 1  83.043  46.127  36.820  1.00  0.00
HETATM2  CAB DR0 1  82.411  45.765  35.421  1.00  0.00
HETATM3  CAC DR0 1  81.495  46.822  34.598  1.00  0.00
HETATM4  CAD DR0 1  80.621  46.369  33.071  1.00  0.00
HETATM5  CAE DR0 1  79.305  47.302  32.172  1.00  0.00
HETATM6  CAF DR0 1  77.939  46.749  31.124  1.00  0.00
HETATM7  CAG DR0 1  76.264  47.439  30.612  1.00  0.00
HETATM8  CAH DR0 1  74.636  46.805  29.962  1.00  0.00
HETATM9  CAI DR0 1  72.805  47.674  30.179  1.00  0.00
HETATM   10  CAJ DR0 1  73.794  48.838  31.123  1.00  0.00
HETATM   11  OAK DR0 1  74.815  49.342  30.292  1.00  0.00
HETATM   12  OAL DR0 1  74.592  48.143  32.194  1.00  0.00
HETATM   13  CAM DR0 1  71.093  47.685  29.486  1.00  0.00
HETATM   14  CAN DR0 1  71.598  47.212  28.208  1.00  0.00
HETATM   15  OAO DR0 1  72.440  48.255  27.735  1.00  0.00
HETATM   16  OAP DR0 1  72.374  46.050  28.399  1.00  0.00
HETATM   17  CAA DRG 2  72.093  46.197  36.714  1.00  0.00
HETATM   18  CAB DRG 2  71.418  45.759  35.400  1.00  0.00
HETATM   19  CAC DRG 2  71.084  46.901  34.417  1.00  0.00
HETATM   20  CAD DRG 2  70.620  46.251  33.139  1.00  0.00
HETATM   21  CAE DRG 2  70.650  47.255  32.000  1.00  0.00
HETATM   22  CAF DRG 2  69.655  46.512  30.955  1.00  0.00
HETATM   23  CAG DRG 2  69.081  47.504  29.843  1.00  0.00
HETATM   24  CAH DRG 2  67.208  47.518  29.256  1.00  0.00
HETATM   25  CAI DRG 2  65.298  47.601  29.691  1.00  0.00
HETATM   26  CAJ DRG 2  65.629  48.362  30.827  1.00  0.00
HETATM   27  OAK DRG 2  65.140  49.590  30.429  1.00  0.00
HETATM   28  OAL DRG 2  64.837  47.815  31.709  1.00  0.00
HETATM   29  CAM DRG 2  63.041  47.557  29.333  1.00  0.00
HETATM   30  CAN DRG 2  62.808  47.023  27.931  1.00  0.00
HETATM   31  OAO DRG 2  63.130  48.142  27.185  1.00  0.00
HETATM   32  OAP DRG 2  63.560  45.894  27.706  1.00  0.00
HETATM   33  CAA DRG 3  61.174  46.188  36.668  1.00  0.00
HETATM   34  CAB DRG 3  60.510  45.777  35.344  1.00  0.00
HETATM   35  CAC DRG 3  60.221  46.928  34.352  1.00  0.00
HETATM   36  CAD DRG 3  59.724  46.337  32.998  1.00  0.00
HETATM   37  CAE DRG 3  60.252  47.307  31.985  1.00  0.00
HETATM   38  CAF DRG 3  61.089  46.606  30.881  1.00  0.00
HETATM   39  CAG DRG 3  60.868  47.564  29.740  1.00  0.00
HETATM   40  CAH DRG 3  58.621  47.652  29.253  1.00  0.00
HETATM   41  CAI DRG 3  56.328  47.703  29.755  1.00  0.00
HETATM   42  CAJ DRG 3  55.914  48.516  30.963  1.00  0.00
HETATM   43  OAK DRG 3  55.050  49.545  30.403  1.00  0.00
HETATM   44  OAL DRG 3  54.945  47.724  31.565  1.00  0.00
HETATM   45  CAM DRG 3  54.420  47.478  29.367  1.00  0.00
HETATM   46  CAN DRG 3  53.587  47.142  27.983  1.00  0.00
HETATM   47  OAO DRG 3  52.713  48.009  27.325  1.00  0.00
HETATM   48  OAP DRG 3  53.396  45.805  27.517  1.00  0.00
HETATM   49  CAA DR1 4  50.257  46.173  36.646  1.00  0.00
HETATM   50  CAB DR1 4  49.673  45.778  35.270  1.00  0.00
HETATM   51  CAC DR1 4  49.360  46.939  34.273  1.00  0.00
HETATM   52  CAD DR1 4  49.270  46.480  32.735  1.00  0.00
HETATM   53  CAE DR1 4  50.289  47.086  31.602  1.00  0.00
HETATM   54  CAF DR1 4  51.813  46.713  31.234  1.00  0.00
HETATM   55  CAG DR1 4  52.487  47.720  29.966  1.00  0.00
HETATM   56  CAH DR1 4  50.870  47.989  29.178  1.00  0.00
HETATM   57  CAI DR1 4  48.982  47.816  29.191  1.00  0.00
HETATM   58  CAJ DR1 4  47.901  48.319  30.192  1.00  0.00
HETATM   59  OAK DR1 4  47.004  49.132  29.503  1.00  0.00
HETATM   60  OAL DR1 4  46.963  47.171  30.588  1.00  0.00
HETATM   61  CAM DR1 4  47.752  46.922  28.157  1.00  0.00
HETATM   62  CAN DR1 4  46.372  47.149  27.020  1.00  0.00
HETATM   63  OAO DR1 4  45.018  47.950  26.877  1.00  0.00
HETATM   64  OAP DR1 4  46.019  46.082  26.137  1.00  0.00
TER
ENDMDL


--
From: "Justin A. Lemkul" 
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" 
Subject: Re: [gmx-users] bad bond in polymer




nicegromacs wrote:
I follow some of the step of 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I 
omitted the change in the .hdb file because I don't have explicit 
hydrogens). Well, I build a polymer with 3 units. The head (H), one 
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, 
but when I add one more repetitive unit (H-R-R-T) I get the following 
error:

Program pdb2gmx, VERSION 3.3.3
Source

Re: [gmx-users] bad bond in polymer

2009-08-14 Thread Justin A. Lemkul 


The problem is in how you handle impropers.  From your previous post, your [DRG] 
entry had the following:


[ impropers ]
  CAG  CAF -CAM  C
 -CAM -CAN -CAI  C
  CAJ  CAI  OAL  O
  CAN  CAM  OAP  O
  CAI  CAH  CAJ  C

The last column needs to correspond to an actual atom name; there may also be 
issues with atom naming, since that previous post also had different atom names 
for DR0, DRG, and DR1 residues.  In the attached .pdb file, you appear to have 
uniform naming between all of the residues.


Be careful which files you are using; it looks like you have made multiple 
attempts.  If things still aren't working out, please post:


1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.

-Justin

nicegromacs wrote:

Hi Justin,

ups!! I am sorry this is the exact .pdb file.

HETATM1  CAA DR0 1  83.043  46.127  36.820  1.00  0.00
HETATM2  CAB DR0 1  82.411  45.765  35.421  1.00  0.00
HETATM3  CAC DR0 1  81.495  46.822  34.598  1.00  0.00
HETATM4  CAD DR0 1  80.621  46.369  33.071  1.00  0.00
HETATM5  CAE DR0 1  79.305  47.302  32.172  1.00  0.00
HETATM6  CAF DR0 1  77.939  46.749  31.124  1.00  0.00
HETATM7  CAG DR0 1  76.264  47.439  30.612  1.00  0.00
HETATM8  CAH DR0 1  74.636  46.805  29.962  1.00  0.00
HETATM9  CAI DR0 1  72.805  47.674  30.179  1.00  0.00
HETATM   10  CAJ DR0 1  73.794  48.838  31.123  1.00  0.00
HETATM   11  OAK DR0 1  74.815  49.342  30.292  1.00  0.00
HETATM   12  OAL DR0 1  74.592  48.143  32.194  1.00  0.00
HETATM   13  CAM DR0 1  71.093  47.685  29.486  1.00  0.00
HETATM   14  CAN DR0 1  71.598  47.212  28.208  1.00  0.00
HETATM   15  OAO DR0 1  72.440  48.255  27.735  1.00  0.00
HETATM   16  OAP DR0 1  72.374  46.050  28.399  1.00  0.00
HETATM   17  CAA DRG 2  72.093  46.197  36.714  1.00  0.00
HETATM   18  CAB DRG 2  71.418  45.759  35.400  1.00  0.00
HETATM   19  CAC DRG 2  71.084  46.901  34.417  1.00  0.00
HETATM   20  CAD DRG 2  70.620  46.251  33.139  1.00  0.00
HETATM   21  CAE DRG 2  70.650  47.255  32.000  1.00  0.00
HETATM   22  CAF DRG 2  69.655  46.512  30.955  1.00  0.00
HETATM   23  CAG DRG 2  69.081  47.504  29.843  1.00  0.00
HETATM   24  CAH DRG 2  67.208  47.518  29.256  1.00  0.00
HETATM   25  CAI DRG 2  65.298  47.601  29.691  1.00  0.00
HETATM   26  CAJ DRG 2  65.629  48.362  30.827  1.00  0.00
HETATM   27  OAK DRG 2  65.140  49.590  30.429  1.00  0.00
HETATM   28  OAL DRG 2  64.837  47.815  31.709  1.00  0.00
HETATM   29  CAM DRG 2  63.041  47.557  29.333  1.00  0.00
HETATM   30  CAN DRG 2  62.808  47.023  27.931  1.00  0.00
HETATM   31  OAO DRG 2  63.130  48.142  27.185  1.00  0.00
HETATM   32  OAP DRG 2  63.560  45.894  27.706  1.00  0.00
HETATM   33  CAA DRG 3  61.174  46.188  36.668  1.00  0.00
HETATM   34  CAB DRG 3  60.510  45.777  35.344  1.00  0.00
HETATM   35  CAC DRG 3  60.221  46.928  34.352  1.00  0.00
HETATM   36  CAD DRG 3  59.724  46.337  32.998  1.00  0.00
HETATM   37  CAE DRG 3  60.252  47.307  31.985  1.00  0.00
HETATM   38  CAF DRG 3  61.089  46.606  30.881  1.00  0.00
HETATM   39  CAG DRG 3  60.868  47.564  29.740  1.00  0.00
HETATM   40  CAH DRG 3  58.621  47.652  29.253  1.00  0.00
HETATM   41  CAI DRG 3  56.328  47.703  29.755  1.00  0.00
HETATM   42  CAJ DRG 3  55.914  48.516  30.963  1.00  0.00
HETATM   43  OAK DRG 3  55.050  49.545  30.403  1.00  0.00
HETATM   44  OAL DRG 3  54.945  47.724  31.565  1.00  0.00
HETATM   45  CAM DRG 3  54.420  47.478  29.367  1.00  0.00
HETATM   46  CAN DRG 3  53.587  47.142  27.983  1.00  0.00
HETATM   47  OAO DRG 3  52.713  48.009  27.325  1.00  0.00
HETATM   48  OAP DRG 3  53.396  45.805  27.517  1.00  0.00
HETATM   49  CAA DR1 4  50.257  46.173  36.646  1.00  0.00
HETATM   50  CAB DR1 4  49.673  45.778  35.270  1.00  0.00
HETATM   51  CAC DR1 4  49.360  46.939  34.273  1.00  0.00
HETATM   52  CAD DR1 4  49.270  46.480  32.735  1.00  0.00
HETATM   53  CAE DR1 4  50.289  47.086  31.602  1.00  0.00
HETATM   54  CAF DR1 4  51.813  46.713  31.234  1.00  0.00
HETATM   55  CAG DR1 4  52.487  47.720  29.966  1.00  0.00
HETATM   56  CAH DR1 4  50.870  47.989  29.178  1.00  0.00
HETATM   57  CAI DR1 4  48.982  47.816  29.191  1.00  0.00
HETATM   58  CAJ DR1 4  47.901  48.319  30.192  1.00  0.00
HETATM   59  OAK DR1 4  47.004  49.132  29.503  1.00  0.00
HETATM   60  OAL DR1 4  46.963  47.171  30.588  1.00  0.00
HETATM   61  CAM DR1 4  47.752  46.922  28.157  1.00  0.00
HETATM   62  CAN DR1 4  46.372  47.149  27.020  1.00  0.00
HETATM   63  OAO DR1 4

Re: [gmx-users] bad bond in polymer

2009-08-14 Thread nicegromacs 

Hi Justin,
Ok, I have done some arrangements to the .rtp file (whit the same pdb file 
DR0-DRG-DRG-DR1) but I still have the same error.


the rtp file is:
[ DRG ]   ;
[ atoms ]
  CAA  CH30.000 1
  CAB  CH20.000  1
  CAC  CH20.000  1
  CAD  CH20.000  1
  CAE  CH20.000  2
  CAF  CH20.000  2
  CAG  CH10.000  3
  CAH  CH20.041  4
  CAI  CH10.107  4
  CAJC0.352  4
  OAK   OM   -0.750  4
  OAL   OM   -0.750  4
  CAM  CH20.044  5
  CANC0.373  5
  OAO   OM   -0.709  5
  OAP   OM   -0.708  5
[ bonds ]
  CAM -CAG
  CAA  CAB
  CAB  CAC
  CAC  CAD
  CAD  CAE
  CAE  CAF
  CAF  CAG
  CAG  CAH
  CAH  CAI
  CAI  CAJ
  CAI  CAM
  CAJ  OAK
  CAJ  OAL
  CAM  CAN
  CAN  OAO
  CAN  OAP
  CAG +CAM
[ impropers ]
  CAG  CAF -CAM  CAH
 -CAM -CAN -CAI  CAG
  CAJ  CAI  OAL  OAK
  CAN  CAM  OAP  OAO
  CAI  CAH  CAJ  CAM

;  head of the polymer

[ DR1 ]
[ atoms ]
  CAA  CH30.000 1
  CAB  CH20.000  1
  CAC  CH20.000  1
  CAD  CH20.000  1
  CAE  CH20.000  2
  CAF  CH20.000  2
  CAG  CH10.000  3
  CAH  CH20.041  4
  CAI  CH10.107  4
  CAJC0.352  4
  OAK   OM   -0.750  4
  OAL   OM   -0.750  4
  CAM  CH20.044  5
  CANC0.373  5
  OAO   OM   -0.709  5
  OAP   OM   -0.708  5
[ bonds ]
  CAA  CAB
  CAB  CAC
  CAC  CAD
  CAD  CAE
  CAE  CAF
  CAF  CAG
  CAG  CAH
  CAH  CAI
  CAI  CAJ
  CAI  CAM
  CAJ  OAK
  CAJ  OAL
  CAM  CAN
  CAN  OAO
  CAN  OAP
  CAG +CAM
[ impropers ]
  CAG  CAF +CAM  CAH
 +CAM +CAN +CAI  CAG
  CAJ  CAI  OAL  OAK
  CAN  CAM  OAP  OAO
  CAI  CAH  CAJ  CAM

; the tail of the polymer
[ DR2 ]
[ atoms ]
  CAA  CH30.000 1
  CAB  CH20.000  1
  CAC  CH20.000  1
  CAD  CH20.000  1
  CAE  CH20.000  2
  CAF  CH20.000  2
  CAG  CH10.000  3
  CAH  CH20.041  4
  CAI  CH10.107  4
  CAJC0.352  4
  OAK   OM   -0.750  4
  OAL   OM   -0.750  4
  CAM  CH20.044  5
  CANC0.373  5
  OAO   OM   -0.709  5
  OAP   OM   -0.708  5
[ bonds ]
  CAM -CAG
  CAA  CAB
  CAB  CAC
  CAC  CAD
  CAD  CAE
  CAE  CAF
  CAF  CAG
  CAG  CAH
  CAH  CAI
  CAI  CAJ
  CAI  CAM
  CAJ  OAK
  CAJ  OAL
  CAM  CAN
  CAN  OAO
  CAN  OAP
[ impropers ]
  CAG  CAF -CAM  CAH
 -CAM -CAN -CAI  CAG
  CAJ  CAI  OAL  OAK
  CAN  CAM  OAP  OAO
  CAI  CAH  CAJ  CAM

--
From: "Justin A. Lemkul" 
Sent: Friday, August 14, 2009 2:46 PM
To: "Gromacs Users' List" 
Subject: Re: [gmx-users] bad bond in polymer



The problem is in how you handle impropers.  From your previous post, your 
[DRG] entry had the following:


[ impropers ]
  CAG  CAF -CAM  C
 -CAM -CAN -CAI  C
  CAJ  CAI  OAL  O
  CAN  CAM  OAP  O
  CAI  CAH  CAJ  C

The last column needs to correspond to an actual atom name; there may also 
be issues with atom naming, since that previous post also had different 
atom names for DR0, DRG, and DR1 residues.  In the attached .pdb file, you 
appear to have uniform naming between all of the residues.


Be careful which files you are using; it looks like you have made multiple 
attempts.  If things still aren't working out, please post:


1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.

-Justin

nicegromacs wrote:

Hi Justin,

ups!! I am sorry this is the exact .pdb file.

HETATM1  CAA DR0 1  83.043  46.127  36.820  1.00  0.00
HETATM2  CAB DR0 1  82.411  45.765  35.421  1.00  0.00
HETATM3  CAC DR0 1  81.495  46.822  34.598  1.00  0.00
HETATM4  CAD DR0 1  80.621  46.369  33.071  1.00  0.00
HETATM5  CAE DR0 1  79.305  47.302  32.172  1.00  0.00
HETATM6  CAF DR0 1  77.939  46.749  31.124  1.00  0.00
HETATM7  CAG DR0 1  76.264  47.439  30.612  1.00  0.00
HETATM8  CAH DR0 1  74.636  46.805  29.962  1.00  0.00
HETATM9  CAI DR0 1  72.805  47.674  30.179  1.00  0.00
HETATM   10  CAJ DR0 1  73.794  48.838  31.123  1.00  0.00
HETATM   11  OAK DR0 1  74.815  49.342  30.292  1.00  0.00
HETATM   12  OAL DR0 1  74.592  48.143  32.194  1.00  0.00
HETATM   13  CAM DR0 1  71.093  47.685  29.486  1.00  0.00
HETATM   14  CAN DR0 1  71.598  47.212  28.208  1.00  0.00
HETATM   15  OAO DR0 1  72.440  48.255  27.735  1.00  0.00
HETATM   16  OAP DR0 1  72.374  46.050  28.399  1.00  0.00
HETATM   17  CAA DRG 2  72.093  46.197  36.714  1.00  0.00
HETATM   18  CAB DRG 2  71.418  45.759  35.400  1.00  0.00
HETATM   19  CAC DRG 2  71.084  46.901  34.417  1.00  0.00
HETATM   20  CAD DRG 2  70.620  46.251  33.139  1.00  0.00
HETATM   21  CAE DRG 2  70.650  47.255  32.000  1.00  0.00
HETATM   22  CAF DRG 2  69.655  46.512  30.955  1.00  0.00
HETATM   23  CAG DRG 2

Re: [gmx-users] bad bond in polymer

2009-08-14 Thread Justin A. Lemkul 



nicegromacs wrote:

Hi Justin,
Ok, I have done some arrangements to the .rtp file (whit the same pdb 
file DR0-DRG-DRG-DR1) but I still have the same error.




Using these .rtp entries with the .pdb file you posted (after adjusting the 
residue names) works for me, using version 4.0.5.  Do you have problems with 
other standard structures?  It was weird that pdb2gmx was spitting out infinite 
residue numbers.  Does your installation pass the test set?


-Justin


the rtp file is:
[ DRG ]   ;
[ atoms ]
  CAA  CH30.000 1
  CAB  CH20.000 1
  CAC  CH20.000 1
  CAD  CH20.000 1
  CAE  CH20.000 2
  CAF  CH20.000 2
  CAG  CH10.000 3
  CAH  CH20.041 4
  CAI  CH10.107 4
  CAJC0.352 4
  OAK   OM   -0.750 4
  OAL   OM   -0.750 4
  CAM  CH20.044 5
  CANC0.373 5
  OAO   OM   -0.709 5
  OAP   OM   -0.708 5
[ bonds ]
  CAM -CAG
  CAA  CAB
  CAB  CAC
  CAC  CAD
  CAD  CAE
  CAE  CAF
  CAF  CAG
  CAG  CAH
  CAH  CAI
  CAI  CAJ
  CAI  CAM
  CAJ  OAK
  CAJ  OAL
  CAM  CAN
  CAN  OAO
  CAN  OAP
  CAG +CAM
[ impropers ]
  CAG  CAF -CAM  CAH
 -CAM -CAN -CAI  CAG
  CAJ  CAI  OAL  OAK
  CAN  CAM  OAP  OAO
  CAI  CAH  CAJ  CAM

;  head of the polymer

[ DR1 ]
[ atoms ]
  CAA  CH30.000 1
  CAB  CH20.000 1
  CAC  CH20.000 1
  CAD  CH20.000 1
  CAE  CH20.000 2
  CAF  CH20.000 2
  CAG  CH10.000 3
  CAH  CH20.041 4
  CAI  CH10.107 4
  CAJC0.352 4
  OAK   OM   -0.750 4
  OAL   OM   -0.750 4
  CAM  CH20.044 5
  CANC0.373 5
  OAO   OM   -0.709 5
  OAP   OM   -0.708 5
[ bonds ]
  CAA  CAB
  CAB  CAC
  CAC  CAD
  CAD  CAE
  CAE  CAF
  CAF  CAG
  CAG  CAH
  CAH  CAI
  CAI  CAJ
  CAI  CAM
  CAJ  OAK
  CAJ  OAL
  CAM  CAN
  CAN  OAO
  CAN  OAP
  CAG +CAM
[ impropers ]
  CAG  CAF +CAM  CAH
 +CAM +CAN +CAI  CAG
  CAJ  CAI  OAL  OAK
  CAN  CAM  OAP  OAO
  CAI  CAH  CAJ  CAM

; the tail of the polymer
[ DR2 ]
[ atoms ]
  CAA  CH30.000 1
  CAB  CH20.000 1
  CAC  CH20.000 1
  CAD  CH20.000 1
  CAE  CH20.000 2
  CAF  CH20.000 2
  CAG  CH10.000 3
  CAH  CH20.041 4
  CAI  CH10.107 4
  CAJC0.352 4
  OAK   OM   -0.750 4
  OAL   OM   -0.750 4
  CAM  CH20.044 5
  CANC0.373 5
  OAO   OM   -0.709 5
  OAP   OM   -0.708 5
[ bonds ]
  CAM -CAG
  CAA  CAB
  CAB  CAC
  CAC  CAD
  CAD  CAE
  CAE  CAF
  CAF  CAG
  CAG  CAH
  CAH  CAI
  CAI  CAJ
  CAI  CAM
  CAJ  OAK
  CAJ  OAL
  CAM  CAN
  CAN  OAO
  CAN  OAP
[ impropers ]
  CAG  CAF -CAM  CAH
 -CAM -CAN -CAI  CAG
  CAJ  CAI  OAL  OAK
  CAN  CAM  OAP  OAO
  CAI  CAH  CAJ  CAM

--
From: "Justin A. Lemkul" 
Sent: Friday, August 14, 2009 2:46 PM
To: "Gromacs Users' List" 
Subject: Re: [gmx-users] bad bond in polymer



The problem is in how you handle impropers.  From your previous post, 
your [DRG] entry had the following:


[ impropers ]
  CAG  CAF -CAM  C
 -CAM -CAN -CAI  C
  CAJ  CAI  OAL  O
  CAN  CAM  OAP  O
  CAI  CAH  CAJ  C

The last column needs to correspond to an actual atom name; there may 
also be issues with atom naming, since that previous post also had 
different atom names for DR0, DRG, and DR1 residues.  In the attached 
.pdb file, you appear to have uniform naming between all of the residues.


Be careful which files you are using; it looks like you have made 
multiple attempts.  If things still aren't working out, please post:


1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.

-Justin

nicegromacs wrote:

Hi Justin,

ups!! I am sorry this is the exact .pdb file.

HETATM1  CAA DR0 1  83.043  46.127  36.820  1.00  0.00
HETATM2  CAB DR0 1  82.411  45.765  35.421  1.00  0.00
HETATM3  CAC DR0 1  81.495  46.822  34.598  1.00  0.00
HETATM4  CAD DR0 1  80.621  46.369  33.071  1.00  0.00
HETATM5  CAE DR0 1  79.305  47.302  32.172  1.00  0.00
HETATM6  CAF DR0 1  77.939  46.749  31.124  1.00  0.00
HETATM7  CAG DR0 1  76.264  47.439  30.612  1.00  0.00
HETATM8  CAH DR0 1  74.636  46.805  29.962  1.00  0.00
HETATM9  CAI DR0 1  72.805  47.674  30.179  1.00  0.00
HETATM   10  CAJ DR0 1  73.794  48.838  31.123  1.00  0.00
HETATM   11  OAK DR0 1  74.815  49.342  30.292  1.00  0.00
HETATM   12  OAL DR0 1  74.592  48.143  32.194  1.00  0.00
HETATM   13  CAM DR0 1  71.093  47.685  29.486  1.00  0.00
HETATM   14  CAN DR0 1  71.598  47.212  28.208  1.00  0.00
HETATM   15  OAO DR0 1  72.440  48.255  27.735  1.00  0.00
HETATM   16  OAP DR0 1  72.374  46.050  28.399  1.00  0.00
HETATM   17  CAA DRG 2  72.093  46.197  36.714  1.00  0.00
HETATM   18  CAB DRG 2  71.418  45.759  35.400  1.00  0.00
HETATM   19

[gmx-users] Unexpected Production of .pdb files

2009-08-14 Thread Warren Gallin 

Hi,

	I am running GROMACS 4.0.5 on a peptide composed of 10 serine  
residues in a water box.


	During the run, there have been several pairs of files being written  
into the working directory, for example:


step20230b_n5.pdb
step20230c_n5.pdb

	When I look at the files in PyMol they appear to contain a slab of  
water, one or two ions and a fragment of the peptide.


	I've gone back and checked and the peptide was intact in the starting  
system that had been energy minimized and had the waters equilibrated.


	This is only happening in one run (Ser10) and not with two other  
decapeptides (Asp10 and Gly10) that have een set up and run identically.


	The run doesn't seem to be affected, it's not throwing errors as far  
as I can see and continues running.


I have not found any mention of this in the manual.

	Is this some weird glitch in my computer (writing intermediate data  
to a file?) or a known behavior of GROMACS under some conditions?


Just trying to understand what's happening.

Warren Gallin
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Re: [gmx-users] Unexpected Production of .pdb files

2009-08-14 Thread Justin A. Lemkul 



Warren Gallin wrote:

Hi,

I am running GROMACS 4.0.5 on a peptide composed of 10 serine 
residues in a water box.


During the run, there have been several pairs of files being written 
into the working directory, for example:


step20230b_n5.pdb
step20230c_n5.pdb

When I look at the files in PyMol they appear to contain a slab of 
water, one or two ions and a fragment of the peptide.


I've gone back and checked and the peptide was intact in the 
starting system that had been energy minimized and had the waters 
equilibrated.


This is only happening in one run (Ser10) and not with two other 
decapeptides (Asp10 and Gly10) that have een set up and run identically.


The run doesn't seem to be affected, it's not throwing errors as far 
as I can see and continues running.


I have not found any mention of this in the manual.

Is this some weird glitch in my computer (writing intermediate data 
to a file?) or a known behavior of GROMACS under some conditions?


Just trying to understand what's happening.



These intermediate files are written when mdrun suspects that a crash might be 
imminent, to allow you to diagnose the problem.  Check your .log file for 
messages related to:


http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

-Justin


Warren Gallin
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Position Restrain md

2009-08-14 Thread Jamie Seyed 
Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein   non-protein
(1) Doesn't that mean everything in the system? I think for this case we can
simply write "system" because system is made by protein and non-protein??
(2) In this case how program recognize which one should restrain and which
one not, because it included all??
(3) This step is required for every system or only proteins??
(4) If I want to make an index file and I specify a group that need to be
constrained, in the generated index file I will get system and all its parts
and an extra part for my specific part that need to be constrain...Is that
ok??
(5) In my case I have a molecule (MOL) and water (SOL), for position
restrain md should I use "tc_grps=MOL   SOL" (according to fws tutorial) or
I need only write "tc_grps=MOL"??  Many Thanks in Advance/Jamie
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Re: [gmx-users] Position Restrain md

2009-08-14 Thread Mark Abraham 

Jamie Seyed wrote:

Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein   non-protein
(1) Doesn't that mean everything in the system? I think for this case we can
simply write "system" because system is made by protein and non-protein??


It includes the whole system, but it is often a good idea not to couple 
groups of heterogeneous heat capacity to the same thermostat. That said, 
if the groups are too small, you get other problems. See also 
http://oldwiki.gromacs.org/index.php/temperature_coupling



(2) In this case how program recognize which one should restrain and which
one not, because it included all??


Temperature coupling has no linkage with position restraints. You 
defined the latter in your .top file.



(3) This step is required for every system or only proteins??


It may or may not be useful in achieving stable equilibration for any 
system. See 
http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation



(4) If I want to make an index file and I specify a group that need to be
constrained, in the generated index file I will get system and all its parts
and an extra part for my specific part that need to be constrain...Is that
ok??


"constraints" are different from "restraints" in GROMACS usage. make_ndx 
does allow you to generate new index groups, but you will need to 
(re-)read the relevant manual sections to understand that neither of 
these algorithms uses index groups. (Or to prove my memory wrong!)



(5) In my case I have a molecule (MOL) and water (SOL), for position
restrain md should I use "tc_grps=MOL   SOL" (according to fws tutorial) or
I need only write "tc_grps=MOL"??  Many Thanks in Advance/Jamie


The latter won't work, for all atoms must be members of a 
temperature-coupling group if any are.


What you actually need is a clear understanding of your strategic 
objective. Hopefully some of the links will move you towards that.


Mark
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Re: [gmx-users] Position Restrain md

2009-08-14 Thread Jamie Seyed 
Hi Mark,
Thanks for the answers. One question still remains for me: in the fws
tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run
grompp followed by mdrun... Am I missing some thing? Because I can not see
it introduces something that to be restrained..?? Would you please let me
know what I am missing here?? Many Thanks in Advance/Jamie
On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham wrote:

> Jamie Seyed wrote:
>
>> Dear all,
>> I have questions regarding the position restrain md. I tried to find the
>> answer of my questions from the mailing list, but it is not clear yet.
>> In the fws tutorial when it says (in the pr.mdp)
>> tc_grps=Protein   non-protein
>> (1) Doesn't that mean everything in the system? I think for this case we
>> can
>> simply write "system" because system is made by protein and non-protein??
>>
>
> It includes the whole system, but it is often a good idea not to couple
> groups of heterogeneous heat capacity to the same thermostat. That said, if
> the groups are too small, you get other problems. See also
> http://oldwiki.gromacs.org/index.php/temperature_coupling
>
> (2) In this case how program recognize which one should restrain and which
>> one not, because it included all??
>>
>
> Temperature coupling has no linkage with position restraints. You defined
> the latter in your .top file.
>
> (3) This step is required for every system or only proteins??
>>
>
> It may or may not be useful in achieving stable equilibration for any
> system. See
> http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
>
> (4) If I want to make an index file and I specify a group that need to be
>> constrained, in the generated index file I will get system and all its
>> parts
>> and an extra part for my specific part that need to be constrain...Is that
>> ok??
>>
>
> "constraints" are different from "restraints" in GROMACS usage. make_ndx
> does allow you to generate new index groups, but you will need to (re-)read
> the relevant manual sections to understand that neither of these algorithms
> uses index groups. (Or to prove my memory wrong!)
>
> (5) In my case I have a molecule (MOL) and water (SOL), for position
>> restrain md should I use "tc_grps=MOL   SOL" (according to fws tutorial)
>> or
>> I need only write "tc_grps=MOL"??  Many Thanks in Advance/Jamie
>>
>
> The latter won't work, for all atoms must be members of a
> temperature-coupling group if any are.
>
> What you actually need is a clear understanding of your strategic
> objective. Hopefully some of the links will move you towards that.
>
> Mark
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Re: [gmx-users] Position Restrain md

2009-08-14 Thread Mark Abraham 

Jamie Seyed wrote:

Hi Mark,
Thanks for the answers. One question still remains for me: in the fws
tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run
grompp followed by mdrun... Am I missing some thing? Because I can not see
it introduces something that to be restrained..?? Would you please let me
know what I am missing here?? Many Thanks in Advance/Jamie


pdb2gmx automatically produces a posre.itp file, whose position 
restraint contents are #included from the .top file it produces, and 
whose function is sensitive to the -DPOSRES option. Search the wiki for 
discussion of this machinery.


Mark


On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham wrote:


Jamie Seyed wrote:


Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein   non-protein
(1) Doesn't that mean everything in the system? I think for this case we
can
simply write "system" because system is made by protein and non-protein??


It includes the whole system, but it is often a good idea not to couple
groups of heterogeneous heat capacity to the same thermostat. That said, if
the groups are too small, you get other problems. See also
http://oldwiki.gromacs.org/index.php/temperature_coupling

(2) In this case how program recognize which one should restrain and which

one not, because it included all??


Temperature coupling has no linkage with position restraints. You defined
the latter in your .top file.

(3) This step is required for every system or only proteins??
It may or may not be useful in achieving stable equilibration for any
system. See
http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

(4) If I want to make an index file and I specify a group that need to be

constrained, in the generated index file I will get system and all its
parts
and an extra part for my specific part that need to be constrain...Is that
ok??


"constraints" are different from "restraints" in GROMACS usage. make_ndx
does allow you to generate new index groups, but you will need to (re-)read
the relevant manual sections to understand that neither of these algorithms
uses index groups. (Or to prove my memory wrong!)

(5) In my case I have a molecule (MOL) and water (SOL), for position

restrain md should I use "tc_grps=MOL   SOL" (according to fws tutorial)
or
I need only write "tc_grps=MOL"??  Many Thanks in Advance/Jamie


The latter won't work, for all atoms must be members of a
temperature-coupling group if any are.

What you actually need is a clear understanding of your strategic
objective. Hopefully some of the links will move you towards that.

Mark
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