Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF

[Mark Abraham]

On 14/05/2012 4:18 PM, Anirban wrote:



On Mon, May 14, 2012 at 11:35 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 14/05/2012 3:52 PM, Anirban wrote:

Hi ALL,

I am trying to simulate a membrane protein system using CHARMM36
FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The
system consists of arounf 1,17,000 atoms. The job runs fine on 5
nodes (5X12=120 cores) using mpirun and gives proper output. But
whenever I try to submit it on more than 5 nodes, the job gets
killed with the following error:


That's likely going to be an issue with the configuration of your
MPI system, or your hardware, or both. Do check your .log file for
evidence of unsuitable DD partiion, though the fact of "turning on
dynamic load balancing" suggest DD partitioning worked OK.

Mark


Hello Mark,

Thanks for the reply.
The .log file reports no error/warning and ends abruptly with the 
following last lines:


That's most consistent with a problem external to GROMACS.

Mark




Making 3D domain decomposition grid 4 x 3 x 9, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  Protein_POPC
  1:  SOL_CL
There are: 117548 Atoms
Charge group distribution at step 0: 358 353 443 966 1106 746 374 351 
352 352 358 454 975 1080 882 381 356 357 357 358 375 770 1101 882 365 
359 358 351 348 487 983 1051 912 377 344 361 363 352 596 1051 1036 
1050 553 351 349 366 352 375 912 1125 1045 478 351 344 356 362 445 971 
1040 959 520 405 355 357 355 639 1032 1072 1096 790 474 353 349 345 
449 1019 1047 971 444 354 357 355 357 391 946 1093 904 375 367 368 349 
349 409 934 1082 867 406 350 350 364 341 398 978 1104 937 415 341 368

Grid: 6 x 7 x 4 cells
Initial temperature: 300.318 K

Started mdrun on node 0 Fri May 11 20:43:52 2012

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
U-BProper Dih.  Improper Dih.  CMAP Dih. 
 LJ-14
8.67972e+046.15820e+041.38445e+03   -1.60452e+03   
 1.44395e+04
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip. 
 Potential
   -5.21377e+044.98413e+04   -1.21372e+06   -8.94296e+04   
-1.14284e+06
Kinetic En.   Total EnergyTemperature Pressure (bar)   Constr. 
rmsd
2.93549e+05   -8.49294e+053.00132e+02   -1.80180e+01   
 1.40708e-05

---

Any suggestion is welcome.

Thanks,

Anirban





-

starting mdrun 'Protein'
5000 steps, 10.0 ps.

NOTE: Turning on dynamic load balancing

Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error


=
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 256
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

=
[proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed
[proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine
error waiting for event
.
.
.

--

Why is this happening? Is it related to DD and PME? How to solve
it? Any suggestion is welcome.
Sorry for re-posting.


Thanks and regards,

Anirban







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Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF

[Anirban]

On Mon, May 14, 2012 at 11:35 AM, Mark Abraham wrote:

>  On 14/05/2012 3:52 PM, Anirban wrote:
>
>  Hi ALL,
>
> I am trying to simulate a membrane protein system using CHARMM36 FF on
> GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
> arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using
> mpirun and gives proper output. But whenever I try to submit it on more
> than 5 nodes, the job gets killed with the following error:
>
>
> That's likely going to be an issue with the configuration of your MPI
> system, or your hardware, or both. Do check your .log file for evidence of
> unsuitable DD partiion, though the fact of "turning on dynamic load
> balancing" suggest DD partitioning worked OK.
>
> Mark
>
>
Hello Mark,

Thanks for the reply.
The .log file reports no error/warning and ends abruptly with the following
last lines:


Making 3D domain decomposition grid 4 x 3 x 9, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  Protein_POPC
  1:  SOL_CL
There are: 117548 Atoms
Charge group distribution at step 0: 358 353 443 966 1106 746 374 351 352
352 358 454 975 1080 882 381 356 357 357 358 375 770 1101 882 365 359 358
351 348 487 983 1051 912 377 344 361 363 352 596 1051 1036 1050 553 351 349
366 352 375 912 1125 1045 478 351 344 356 362 445 971 1040 959 520 405 355
357 355 639 1032 1072 1096 790 474 353 349 345 449 1019 1047 971 444 354
357 355 357 391 946 1093 904 375 367 368 349 349 409 934 1082 867 406 350
350 364 341 398 978 1104 937 415 341 368
Grid: 6 x 7 x 4 cells
Initial temperature: 300.318 K

Started mdrun on node 0 Fri May 11 20:43:52 2012

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
U-BProper Dih.  Improper Dih.  CMAP Dih.  LJ-14
8.67972e+046.15820e+041.38445e+03   -1.60452e+031.44395e+04
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
   -5.21377e+044.98413e+04   -1.21372e+06   -8.94296e+04   -1.14284e+06
Kinetic En.   Total EnergyTemperature Pressure (bar)   Constr. rmsd
2.93549e+05   -8.49294e+053.00132e+02   -1.80180e+011.40708e-05
---

Any suggestion is welcome.

Thanks,

Anirban


>
>
>
> -
>
> starting mdrun 'Protein'
> 5000 steps, 10.0 ps.
>
> NOTE: Turning on dynamic load balancing
>
> Fatal error in MPI_Sendrecv: Other MPI error
> Fatal error in MPI_Sendrecv: Other MPI error
> Fatal error in MPI_Sendrecv: Other MPI error
>
>
> =
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 256
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> =
> [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb
> (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed
> [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event
> (./tools/demux/demux_poll.c:77): callback returned error status
> [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error
> waiting for event
> .
> .
> .
>
> --
>
> Why is this happening? Is it related to DD and PME? How to solve it? Any
> suggestion is welcome.
> Sorry for re-posting.
>
>
> Thanks and regards,
>
> Anirban
>
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at
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Re: [gmx-users] DSSP download,installation and dssp plot

[Mark Abraham]

On 14/05/2012 4:14 PM, bunty xy wrote:

Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
get the dssp plot.


This forum is for GROMACS-related questions. It is not apparent to me 
that the plot you seek is GROMACS-related. Perhaps another forum, or the 
DSSP documentation is what you need.


Mark
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[gmx-users] DSSP download,installation and dssp plot

[bunty xy]

Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
get the dssp plot.


Thanks
bunty
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Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF

[Mark Abraham]

On 14/05/2012 3:52 PM, Anirban wrote:

Hi ALL,

I am trying to simulate a membrane protein system using CHARMM36 FF on 
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists 
of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 
cores) using mpirun and gives proper output. But whenever I try to 
submit it on more than 5 nodes, the job gets killed with the following 
error:


That's likely going to be an issue with the configuration of your MPI 
system, or your hardware, or both. Do check your .log file for evidence 
of unsuitable DD partiion, though the fact of "turning on dynamic load 
balancing" suggest DD partitioning worked OK.


Mark



-

starting mdrun 'Protein'
5000 steps, 10.0 ps.

NOTE: Turning on dynamic load balancing

Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error

=
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 256
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=
[proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb 
(./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed
[proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event 
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error 
waiting for event

.
.
.
--

Why is this happening? Is it related to DD and PME? How to solve it? 
Any suggestion is welcome.

Sorry for re-posting.


Thanks and regards,

Anirban






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Re: [gmx-users] User defined potential

[Mark Abraham]

On 14/05/2012 2:24 PM, mohan maruthi sena wrote:

Hi all,
   I want to define a potential form and give it as input for 
which i have seen manual ,thought gromacs table option is fine, i have 
an example of generating 9-6 potential form , My question is how to 
generate table.xvg, what is the command to generate table.xvg from 
code table.c.


There's no general way to generate new tables from within GROMACS. Some 
already exist in the $GMXLIB/share folder. mdrun -debug will write out 
the tables it is using.


Otherwise, working out how to take a suitable spreadsheet you have 
created and export to a text file is often the most straightforward 
procedure.


Mark
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[gmx-users] mdrun_mpi issue with CHARMM36 FF

[Anirban]

Hi ALL,

I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using
mpirun and gives proper output. But whenever I try to submit it on more
than 5 nodes, the job gets killed with the following error:

-

starting mdrun 'Protein'
5000 steps, 10.0 ps.

NOTE: Turning on dynamic load balancing

Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error

=
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 256
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=
[proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed
[proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error
waiting for event
.
.
.
--

Why is this happening? Is it related to DD and PME? How to solve it? Any
suggestion is welcome.
Sorry for re-posting.


Thanks and regards,

Anirban
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[gmx-users] User defined potential

[mohan maruthi sena]

Hi all,
   I want to define a potential form and give it as input for which
i have seen manual ,thought gromacs table option is fine, i have an example
of generating 9-6 potential form , My question is how to generate
table.xvg, what is the command to generate table.xvg from code table.c.


with regards,
Mohan
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[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

[Sangita Kachhap]

t;? > >> [ atoms ]
>>? > >> ; name type charge chargegroup
>>? > >> C C 0.4500 0
>>? > >> O O -0.5700 0
>>? > >> [ bonds ]
>>? > >> ; ai aj fu b0 kb, b0 kb
>>? > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>>? > >>
>>? > >> [ pairs ]
>>? > >> ; ai aj fu
>>? > >>
>>? > >> [ angles ]
>>? > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>>? > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>>? > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>>? > >>
>>? > >> [ dihedrals ]
>>? > >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>>? > >>
>>? > >> But when I do what I described, I face this fatal error:
>>? > >> Fatal error:
>>? > >> No atoms found in .rtp file in residue pairs
>>? > >>
>>? > >> Would you help me with this problem? Did I add the formyl in a wrong
>> way?
>>? > >>
>>? > >
>>? > > Your [pairs] directive is empty, hence the error. Your [dihedrals]
>> directive
>>? > > will also produce the same error. There are no possible pairs in a unit
>>? > > containing so few atoms, so you don't even need this. You may need to
>> define
>>? > > dihedrals, however, but they also depend upon the next residue.
>>? > >
>>? > > You also have several other mistakes:
>>? > >
>>? > > 1. A formyl group has a proton on it; yours has none
>>? > > 2. Your net charge on the formyl group is not zero, though this may or
>> may not
>>? > > be a consequence of point #1
>>? > > 3. There is no connectivity information for linking to the next residue,
>> which
>>? > > will mean the formyl group will not be chemically bonded. This also
>> affects
>> your
>>? > > dihedrals.
>>? > >
>>? >
>>? > Another that I just caught as I hit send:
>>? >
>>? > 4. In your [bonds] and [angles] directives, you use atom numbers - they
>> should
>>? > be names
>>? >
>>? > -Justin
>>? >
>>? > --
>>? > 
>>? >
>>? > Justin A. Lemkul, Ph.D.
>>? > Department of Biochemistry
>>? > Virginia Tech
>>? > Blacksburg, VA
>>? > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>? > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>? >
>>? > 
>>? > --
>>? > gmx-users mailing list gmx-users@gromacs.org 
>><mailto:gmx-users@gromacs.org>
>> <mailto:gmx-users@gromacs.org <mailto: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
>> <mailto:gmx-users-requ...@gromacs.org>
>>? > <mailto:gmx-users-requ...@gromacs.org
>> <mailto:gmx-users-requ...@gromacs.org>>.
>>? > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>? >
>>? >
>>
>> --
>> 
>>
>> Justin A. Lemkul, Ph.D.
>> 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-users@gromacs.org <mailto:gmx-users@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>> before posting!
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>> <mailto:gmx-users-requ...@gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> 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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> End of gmx-users Digest, Vol 97, Issue 87
> *
>


Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH

__
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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Re: [gmx-users] Re: Should I use continuation = yes in my production dynamics following equilibration?

[Justin A. Lemkul]

On 5/13/12 9:54 PM, Andrew DeYoung wrote:

Hi Justin,

Thanks so much!  :-)

I checked, and I am using no constraints.  However, what if I were?  If I
did have constraints, then what would you recommend for the continuation
keyword?



Per the description in the manual, it should be set to "yes" in the case of 
constraints.


-Justin

--


Justin A. Lemkul, Ph.D.
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] Re: Should I use continuation = yes in my production dynamics following equilibration?

[Andrew DeYoung]

Hi Justin,

Thanks so much!  :-)

I checked, and I am using no constraints.  However, what if I were?  If I
did have constraints, then what would you recommend for the continuation
keyword?

Thanks!

Andrew DeYoung
Carnegie Mellon University 

---
If not using constraints, the continuation keyword is irrelevant.  The key
is to be sure there are truly no constraints, including any that use SHAKE
or LINCS (i.e. a solute) or SETTLE (water).  The water models present in
Gromacs should all be rigid (i.e. constrained using SETTLE).  But if you're
sure there are no constraints and that this representation is proper, then
you can ignore the "continuation" keyword.  Saying you "think" there are no
constraints means there is uncertainty, which means you have some checking
to do ;) 

-Justin 

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Re: [gmx-users] Should I use continuation = yes in my production dynamics following equilibration?

[Justin A. Lemkul]

On 5/13/12 9:11 PM, Andrew DeYoung wrote:

Greetings,

I am running 5 ns of equilibration followed by 10 ns of production dynamics.
Equilibration and production dynamics differ only in the number of steps and
the frequency of saving the positions, velocities, forces, and energies.  To
conserve disk space, I set nstxout = nstvout = nstfout = nstenergy to some
high value, such as 100 (in equilibration.mdp), for equilibration.  Then


You can set them to zero to completely eliminate output, if you need to.


for production dynamics, I set nstxout = nstvout = nstfout = nstenergy to
some relatively low value, such as 100 (in dynamics.mdp), because it is from
these data that I will do property analysis.

So, to do this, I have been using a workflow like this:
(1) For equilibration, feed equilibration.mdp to grompp using "-f".  Then
run mdrun, saving the checkpoints to state.cpt.
(2) For production dynamics, feed dynamics.mdp to grompp using "-f".  Also,
feed state.cpt to grompp using "-t".

where equilibration.mdp and dynamics.mdp contain different values of nsteps
and of nstxout, nstvout, nstfout, and nstenergy.

My question is, to do this sort of continuation (where I'm ONLY changing
nsteps, nstxout, nstvout, nstfout, and nstenergy), should I use
"continuation = yes"?

The manual gives this description of continuation:

"This option was formerly known as unconstrained_start.

no: apply constraints to the start configuration and reset shells

yes: do not apply constraints to the start configuration and do not reset
shells, useful for exact coninuation and reruns"

I do not think that my system has any constraints, since all the bonds in
all molecules are flexible, with force constants specified in the .itp
files.  If this is the case, then should I use continuation = yes?  Or,
since I do not have constraints in my system, will it perhaps not make a
difference whether continuation is yes or no?  Do you have any
recommendations?



If not using constraints, the continuation keyword is irrelevant.  The key is to 
be sure there are truly no constraints, including any that use SHAKE or LINCS 
(i.e. a solute) or SETTLE (water).  The water models present in Gromacs should 
all be rigid (i.e. constrained using SETTLE).  But if you're sure there are no 
constraints and that this representation is proper, then you can ignore the 
"continuation" keyword.  Saying you "think" there are no constraints means there 
is uncertainty, which means you have some checking to do ;)


-Justin

--


Justin A. Lemkul, Ph.D.
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] Should I use continuation = yes in my production dynamics following equilibration?

[Andrew DeYoung]

Greetings,

I am running 5 ns of equilibration followed by 10 ns of production dynamics.
Equilibration and production dynamics differ only in the number of steps and
the frequency of saving the positions, velocities, forces, and energies.  To
conserve disk space, I set nstxout = nstvout = nstfout = nstenergy to some
high value, such as 100 (in equilibration.mdp), for equilibration.  Then
for production dynamics, I set nstxout = nstvout = nstfout = nstenergy to
some relatively low value, such as 100 (in dynamics.mdp), because it is from
these data that I will do property analysis. 

So, to do this, I have been using a workflow like this:
(1) For equilibration, feed equilibration.mdp to grompp using "-f".  Then
run mdrun, saving the checkpoints to state.cpt.
(2) For production dynamics, feed dynamics.mdp to grompp using "-f".  Also,
feed state.cpt to grompp using "-t".  

where equilibration.mdp and dynamics.mdp contain different values of nsteps
and of nstxout, nstvout, nstfout, and nstenergy.  

My question is, to do this sort of continuation (where I'm ONLY changing
nsteps, nstxout, nstvout, nstfout, and nstenergy), should I use
"continuation = yes"?

The manual gives this description of continuation: 

"This option was formerly known as unconstrained_start.

no: apply constraints to the start configuration and reset shells

yes: do not apply constraints to the start configuration and do not reset
shells, useful for exact coninuation and reruns"

I do not think that my system has any constraints, since all the bonds in
all molecules are flexible, with force constants specified in the .itp
files.  If this is the case, then should I use continuation = yes?  Or,
since I do not have constraints in my system, will it perhaps not make a
difference whether continuation is yes or no?  Do you have any
recommendations? 

Thank you very much for your time! 

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Justin A. Lemkul]

On 5/13/12 2:17 PM, Shima Arasteh wrote:

But if the hydrogen has charge and its charge is not zero, then the total charge
of formyl wouldn't be zero! Make sense?




This is precisely why I've told you several times that you need to reconsider 
how you've done your parameterization.  If you run formaldehyde through 
SwissParam, it will not give you the parameters you need for a formyl group 
attached to the N-terminus of the protein.  You can't parameterize one molecule 
and then hope to hack its topology apart to create something different.


What you almost certainly need to do is parameterize a new amino acid that has a 
formyl group attached to its alpha amino group.  The .rtp entry thus becomes 
more complex because you have an entirely new amino acid.


-Justin


Sincerely,
Shima

*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Sunday, May 13, 2012 9:44 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs



On 5/13/12 1:06 PM, Shima Arasteh wrote:
 > Even in gromos87, if I want to make a .rtp file for formyl, I need to put H 
atom
 > in it? I mean, defining all atoms of a residue is necessary? Aren't the 
hydrogen
 > atoms set by the gromacs package?
 >

No. The presence of hydrogen atoms is set by the force field, not the software
that makes use of the force fields. In the Gromos force fields (and I certainly
hope you're not using Gromos87, as it is ancient and better options are
available), polar H atoms are explicitly represented. In the case of an
aldehyde, I would strongly suspect you need an explicit H. I believe there have
been recent publications regarding extensions of Gromos96 (note, NOT Gromos87)
that include such organic groups. Using those parameters may speed your
progress. If my recollection is incorrect and such parameters do not exist, you
need to derive them yourself.

-Justin

 > Cheers,
 > Shima
 >
 > 

 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
 > *Sent:* Sunday, May 13, 2012 8:36 PM
 > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
residue pairs
 >
 >
 >
 > On 5/13/12 11:43 AM, Shima Arasteh wrote:
 > > Again thanks for all your replies.
 > > As I got through your advices, I found that the atoms contribute in making
bonds
 > > and angles in a residue , or make dihedrals in a residue ( or with atoms in
next
 > > ones) plus the charge of a the residue should be defined properly in .rtp 
files
 > > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
 > > So I arranged this lines to define formyl in .rtp file. And I got the 
topology.
 > > But there are some questions for me here:
 > >
 > > 1. How can I be sure the formyl which I defined is correct? Is getting the
 > > topology is enough to be sure of the correct output?
 > >
 >
 > It is incorrect. As I said before, a formyl group is an aldehyde and has an H
 > atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
 > with an incomplete carbon valence.
 >
 > http://en.wikipedia.org/wiki/Aldehyde
 >
 > > The .rtp file for formyl is as below:
 > > [ For ]
 > > [ atoms ]
 > > ; name type charge chargegroup
 > > C CTL1 0.5700 0
 > > O O -0.5700 0
 > > [angles ]
 > > ai aj ak
 > > O C +N
 > > [ bonds ]
 > > C O
 > > C +N
 > >
 > > [ dihedrals ]
 > > O C +N +CA
 > >
 >
 > Aside from the missing atom (and resulting missing bonds, angles, and 
dihedral),
 > the format of this entry is OK.
 >
 > > 2. There are lots of numbers in .itp file which I got through the 
swissparam.
 > > But I think the charge of atoms may be useful in this file and also I can 
just
 > > find the atoms contribute in bonds and angles and . Am I right? Or I
may get
 > > some other useful information which I can get through the files of 
swissparam?
 > >
 >
 > If the existing bonded parameters for each interaction type (in ffbonded.itp)
 > are sufficient for defining these interactions, then you can omit the 
content of
 > the .itp file you've been using in the .rtp entry and rely on the force 
field to
 > look up those values. There may be some interactions that are not in 
agreement
 > (or do not exist), in which case you need to either define these parameters 
in
 > the .rtp entry itself or in ffbonded.itp so that they will be detected by 
grompp
 > later.
 >
 > -Justin
 >
 > > Thanks in advance, and sorry for disturbing you friends.
 > > Shima
 > >
 > >

 > > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>
>>
 > > *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>
 > >>
 > > *Sent:* Sat

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Shima Arasteh]

But if the hydrogen has charge and its charge is not zero, then the total 
charge of formyl wouldn't be zero! Make sense?



 
Sincerely,
Shima



 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Sunday, May 13, 2012 9:44 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs
 


On 5/13/12 1:06 PM, Shima Arasteh wrote:
> Even in gromos87, if I want to make a .rtp file for formyl, I need to put H 
> atom
> in it? I mean, defining all atoms of a residue is necessary? Aren't the 
> hydrogen
> atoms set by the gromacs package?
>

No.  The presence of hydrogen atoms is set by the force field, not the software 
that makes use of the force fields.  In the Gromos force fields (and I 
certainly 
hope you're not using Gromos87, as it is ancient and better options are 
available), polar H atoms are explicitly represented.  In the case of an 
aldehyde, I would strongly suspect you need an explicit H.  I believe there 
have 
been recent publications regarding extensions of Gromos96 (note, NOT Gromos87) 
that include such organic groups.  Using those parameters may speed your 
progress.  If my recollection is incorrect and such parameters do not exist, 
you 
need to derive them yourself.

-Justin

> Cheers,
> Shima
>
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Sunday, May 13, 2012 8:36 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in 
> residue pairs
>
>
>
> On 5/13/12 11:43 AM, Shima Arasteh wrote:
>  > Again thanks for all your replies.
>  > As I got through your advices, I found that the atoms contribute in making 
>bonds
>  > and angles in a residue , or make dihedrals in a residue ( or with atoms 
>in next
>  > ones) plus the charge of a the residue should be defined properly in .rtp 
>files
>  > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
>  > So I arranged this lines to define formyl in .rtp file. And I got the 
>topology.
>  > But there are some questions for me here:
>  >
>  > 1. How can I be sure the formyl which I defined is correct? Is getting the
>  > topology is enough to be sure of the correct output?
>  >
>
> It is incorrect. As I said before, a formyl group is an aldehyde and has an H
> atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
> with an incomplete carbon valence.
>
> http://en.wikipedia.org/wiki/Aldehyde
>
>  > The .rtp file for formyl is as below:
>  > [ For ]
>  > [ atoms ]
>  > ; name type charge chargegroup
>  > C CTL1 0.5700 0
>  > O O -0.5700 0
>  > [angles ]
>  > ai aj ak
>  > O C +N
>  > [ bonds ]
>  > C O
>  > C +N
>  >
>  > [ dihedrals ]
>  > O C +N +CA
>  >
>
> Aside from the missing atom (and resulting missing bonds, angles, and 
> dihedral),
> the format of this entry is OK.
>
>  > 2. There are lots of numbers in .itp file which I got through the 
>swissparam.
>  > But I think the charge of atoms may be useful in this file and also I can 
>just
>  > find the atoms contribute in bonds and angles and . Am I right? Or I 
>may get
>  > some other useful information which I can get through the files of 
>swissparam?
>  >
>
> If the existing bonded parameters for each interaction type (in ffbonded.itp)
> are sufficient for defining these interactions, then you can omit the content 
> of
> the .itp file you've been using in the .rtp entry and rely on the force field 
> to
> look up those values. There may be some interactions that are not in agreement
> (or do not exist), in which case you need to either define these parameters in
> the .rtp entry itself or in ffbonded.itp so that they will be detected by 
> grompp
> later.
>
> -Justin
>
>  > Thanks in advance, and sorry for disturbing you friends.
>  > Shima
>  >
>  > 
>
>  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
>  > *To:* Discussion list for GROMACS users  >
>  > *Sent:* Saturday, May 12, 2012 10:12 PM
>  > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
>  >
>  >
>  >
>  > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>  > >
>  > >
>  > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
>  > >> Dear gmx users,
>  > >>
>  > >> I want to simulate a peptide in water. The peptide has a formyl residue 
>as the
>  > >> N-terminus. I got the parameters of it and then add it to the .rtp file 
>of
>  > >> charmm36.ff as below:
>  > >>
>  > >> [ For ]
>  > >> [ atoms ]
>  > >> ; name type charge chargegroup
>  > >> C C 0.4500 0
>  > >> O O -0.5700 0
>  > >> [ bonds ]
>  > >> ; ai aj fu b0 kb, b0 kb
>  > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>  > >>
>  > >> [ pairs ]
>  > >> ; ai aj fu
>  > >>
>  > >> [ angles ]
>  > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>  > >> 2 1 3 1 123.4390 403.48 123.4390

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Shima Arasteh]

 
Thanks,
It was just a question and I prefer to use the CHARMM36. 



 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Sunday, May 13, 2012 9:44 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs
 


On 5/13/12 1:06 PM, Shima Arasteh wrote:
> Even in gromos87, if I want to make a .rtp file for formyl, I need to put H 
> atom
> in it? I mean, defining all atoms of a residue is necessary? Aren't the 
> hydrogen
> atoms set by the gromacs package?
>

No.  The presence of hydrogen atoms is set by the force field, not the software 
that makes use of the force fields.  In the Gromos force fields (and I 
certainly 
hope you're not using Gromos87, as it is ancient and better options are 
available), polar H atoms are explicitly represented.  In the case of an 
aldehyde, I would strongly suspect you need an explicit H.  I believe there 
have 
been recent publications regarding extensions of Gromos96 (note, NOT Gromos87) 
that include such organic groups.  Using those parameters may speed your 
progress.  If my recollection is incorrect and such parameters do not exist, 
you 
need to derive them yourself.

-Justin

> Cheers,
> Shima
>
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Sunday, May 13, 2012 8:36 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in 
> residue pairs
>
>
>
> On 5/13/12 11:43 AM, Shima Arasteh wrote:
>  > Again thanks for all your replies.
>  > As I got through your advices, I found that the atoms contribute in making 
>bonds
>  > and angles in a residue , or make dihedrals in a residue ( or with atoms 
>in next
>  > ones) plus the charge of a the residue should be defined properly in .rtp 
>files
>  > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
>  > So I arranged this lines to define formyl in .rtp file. And I got the 
>topology.
>  > But there are some questions for me here:
>  >
>  > 1. How can I be sure the formyl which I defined is correct? Is getting the
>  > topology is enough to be sure of the correct output?
>  >
>
> It is incorrect. As I said before, a formyl group is an aldehyde and has an H
> atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
> with an incomplete carbon valence.
>
> http://en.wikipedia.org/wiki/Aldehyde
>
>  > The .rtp file for formyl is as below:
>  > [ For ]
>  > [ atoms ]
>  > ; name type charge chargegroup
>  > C CTL1 0.5700 0
>  > O O -0.5700 0
>  > [angles ]
>  > ai aj ak
>  > O C +N
>  > [ bonds ]
>  > C O
>  > C +N
>  >
>  > [ dihedrals ]
>  > O C +N +CA
>  >
>
> Aside from the missing atom (and resulting missing bonds, angles, and 
> dihedral),
> the format of this entry is OK.
>
>  > 2. There are lots of numbers in .itp file which I got through the 
>swissparam.
>  > But I think the charge of atoms may be useful in this file and also I can 
>just
>  > find the atoms contribute in bonds and angles and . Am I right? Or I 
>may get
>  > some other useful information which I can get through the files of 
>swissparam?
>  >
>
> If the existing bonded parameters for each interaction type (in ffbonded.itp)
> are sufficient for defining these interactions, then you can omit the content 
> of
> the .itp file you've been using in the .rtp entry and rely on the force field 
> to
> look up those values. There may be some interactions that are not in agreement
> (or do not exist), in which case you need to either define these parameters in
> the .rtp entry itself or in ffbonded.itp so that they will be detected by 
> grompp
> later.
>
> -Justin
>
>  > Thanks in advance, and sorry for disturbing you friends.
>  > Shima
>  >
>  > 
>
>  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
>  > *To:* Discussion list for GROMACS users  >
>  > *Sent:* Saturday, May 12, 2012 10:12 PM
>  > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
>  >
>  >
>  >
>  > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>  > >
>  > >
>  > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
>  > >> Dear gmx users,
>  > >>
>  > >> I want to simulate a peptide in water. The peptide has a formyl residue 
>as the
>  > >> N-terminus. I got the parameters of it and then add it to the .rtp file 
>of
>  > >> charmm36.ff as below:
>  > >>
>  > >> [ For ]
>  > >> [ atoms ]
>  > >> ; name type charge chargegroup
>  > >> C C 0.4500 0
>  > >> O O -0.5700 0
>  > >> [ bonds ]
>  > >> ; ai aj fu b0 kb, b0 kb
>  > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>  > >>
>  > >> [ pairs ]
>  > >> ; ai aj fu
>  > >>
>  > >> [ angles ]
>  > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>  > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>  > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>  > >>
>  > >> [ 

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Justin A. Lemkul]

On 5/13/12 1:06 PM, Shima Arasteh wrote:

Even in gromos87, if I want to make a .rtp file for formyl, I need to put H atom
in it? I mean, defining all atoms of a residue is necessary? Aren't the hydrogen
atoms set by the gromacs package?



No.  The presence of hydrogen atoms is set by the force field, not the software 
that makes use of the force fields.  In the Gromos force fields (and I certainly 
hope you're not using Gromos87, as it is ancient and better options are 
available), polar H atoms are explicitly represented.  In the case of an 
aldehyde, I would strongly suspect you need an explicit H.  I believe there have 
been recent publications regarding extensions of Gromos96 (note, NOT Gromos87) 
that include such organic groups.  Using those parameters may speed your 
progress.  If my recollection is incorrect and such parameters do not exist, you 
need to derive them yourself.


-Justin


Cheers,
Shima


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Sunday, May 13, 2012 8:36 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs



On 5/13/12 11:43 AM, Shima Arasteh wrote:
 > Again thanks for all your replies.
 > As I got through your advices, I found that the atoms contribute in making 
bonds
 > and angles in a residue , or make dihedrals in a residue ( or with atoms in 
next
 > ones) plus the charge of a the residue should be defined properly in .rtp 
files
 > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
 > So I arranged this lines to define formyl in .rtp file. And I got the 
topology.
 > But there are some questions for me here:
 >
 > 1. How can I be sure the formyl which I defined is correct? Is getting the
 > topology is enough to be sure of the correct output?
 >

It is incorrect. As I said before, a formyl group is an aldehyde and has an H
atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
with an incomplete carbon valence.

http://en.wikipedia.org/wiki/Aldehyde

 > The .rtp file for formyl is as below:
 > [ For ]
 > [ atoms ]
 > ; name type charge chargegroup
 > C CTL1 0.5700 0
 > O O -0.5700 0
 > [angles ]
 > ai aj ak
 > O C +N
 > [ bonds ]
 > C O
 > C +N
 >
 > [ dihedrals ]
 > O C +N +CA
 >

Aside from the missing atom (and resulting missing bonds, angles, and dihedral),
the format of this entry is OK.

 > 2. There are lots of numbers in .itp file which I got through the swissparam.
 > But I think the charge of atoms may be useful in this file and also I can 
just
 > find the atoms contribute in bonds and angles and . Am I right? Or I may 
get
 > some other useful information which I can get through the files of 
swissparam?
 >

If the existing bonded parameters for each interaction type (in ffbonded.itp)
are sufficient for defining these interactions, then you can omit the content of
the .itp file you've been using in the .rtp entry and rely on the force field to
look up those values. There may be some interactions that are not in agreement
(or do not exist), in which case you need to either define these parameters in
the .rtp entry itself or in ffbonded.itp so that they will be detected by grompp
later.

-Justin

 > Thanks in advance, and sorry for disturbing you friends.
 > Shima
 >
 > 

 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
 > *Sent:* Saturday, May 12, 2012 10:12 PM
 > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
residue pairs
 >
 >
 >
 > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
 > >
 > >
 > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
 > >> Dear gmx users,
 > >>
 > >> I want to simulate a peptide in water. The peptide has a formyl residue 
as the
 > >> N-terminus. I got the parameters of it and then add it to the .rtp file of
 > >> charmm36.ff as below:
 > >>
 > >> [ For ]
 > >> [ atoms ]
 > >> ; name type charge chargegroup
 > >> C C 0.4500 0
 > >> O O -0.5700 0
 > >> [ bonds ]
 > >> ; ai aj fu b0 kb, b0 kb
 > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
 > >>
 > >> [ pairs ]
 > >> ; ai aj fu
 > >>
 > >> [ angles ]
 > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
 > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
 > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
 > >>
 > >> [ dihedrals ]
 > >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
 > >>
 > >> But when I do what I described, I face this fatal error:
 > >> Fatal error:
 > >> No atoms found in .rtp file in residue pairs
 > >>
 > >> Would you help me with this problem? Did I add the formyl in a wrong way?
 > >>
 > >
 > > Your [pairs] directive is empty, hence the error. Your [dihedrals] 
directive
 > > will also produce the same error. There are no possible pairs in a unit
 > > containing so few atoms, so you don't even need this. You may nee

Re: [gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

[Justin A. Lemkul]

On 5/13/12 12:52 PM, Sangita Kachhap wrote:

Hello all

I am running GROMACS Tutorial: KALP15 in POPC
I have compeleted production run 1 ns now I want to extend it for next 1 ns.
For this I have used commond:

tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt

I am getting files are:
ener.edr
md.log
state.cpt
state_prev.cpt
traj.trr
traj.xtc
confout.gro

During first 1 ns production I have got all files with prefix  md_0_1.
How I can get it (prefix md_0_2. for all the above files)in next 1 ns production
run.

Anyone please suggest.



Note the use of -deffnm in the tutorial to set default output names.  If you 
want your files to be called "md_0_2.(extension)" then you need to run:


mdrun -deffnm md_0_2 -cpi md_0_1.cpt

-Justin

--


Justin A. Lemkul, Ph.D.
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] Fatal error: No atoms found in .rtp file in residue pairs

[Justin A. Lemkul]

On 5/13/12 12:42 PM, Shima Arasteh wrote:

OK, so I entered the H atom corresponding to the structure and then changed the
file as below,

[ For ]
[ atoms ]
; name type charge charge group
C CTL1 0.5700 0
O O -0.5700 0
H HC 0.00 0



I find it highly unlikely that a zero charge should be assigned to this proton. 
 The .itp file you posted before from SwissParam was for formaldehyde, which 
suggests to me you haven't properly parameterized the species you're looking for 
and now you're trying to hack something together.  Don't try to do that; your 
parameters will be junk.  Parameterize the right species once and proceed from 
there.



[angles ]
ai aj ak
O C +N
O C H

[ bonds ]
C O
C +N
C H

[ dihedrals ]
O C +N +CA
H C +N +H



There are other possible dihedrals here.

-Justin





*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Sunday, May 13, 2012 8:36 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs



On 5/13/12 11:43 AM, Shima Arasteh wrote:
 > Again thanks for all your replies.
 > As I got through your advices, I found that the atoms contribute in making 
bonds
 > and angles in a residue , or make dihedrals in a residue ( or with atoms in 
next
 > ones) plus the charge of a the residue should be defined properly in .rtp 
files
 > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
 > So I arranged this lines to define formyl in .rtp file. And I got the 
topology.
 > But there are some questions for me here:
 >
 > 1. How can I be sure the formyl which I defined is correct? Is getting the
 > topology is enough to be sure of the correct output?
 >

It is incorrect. As I said before, a formyl group is an aldehyde and has an H
atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
with an incomplete carbon valence.

http://en.wikipedia.org/wiki/Aldehyde

 > The .rtp file for formyl is as below:
 > [ For ]
 > [ atoms ]
 > ; name type charge chargegroup
 > C CTL1 0.5700 0
 > O O -0.5700 0
 > [angles ]
 > ai aj ak
 > O C +N
 > [ bonds ]
 > C O
 > C +N
 >
 > [ dihedrals ]
 > O C +N +CA
 >

Aside from the missing atom (and resulting missing bonds, angles, and dihedral),
the format of this entry is OK.

 > 2. There are lots of numbers in .itp file which I got through the swissparam.
 > But I think the charge of atoms may be useful in this file and also I can 
just
 > find the atoms contribute in bonds and angles and . Am I right? Or I may 
get
 > some other useful information which I can get through the files of 
swissparam?
 >

If the existing bonded parameters for each interaction type (in ffbonded.itp)
are sufficient for defining these interactions, then you can omit the content of
the .itp file you've been using in the .rtp entry and rely on the force field to
look up those values. There may be some interactions that are not in agreement
(or do not exist), in which case you need to either define these parameters in
the .rtp entry itself or in ffbonded.itp so that they will be detected by grompp
later.

-Justin

 > Thanks in advance, and sorry for disturbing you friends.
 > Shima
 >
 > 

 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
 > *Sent:* Saturday, May 12, 2012 10:12 PM
 > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
residue pairs
 >
 >
 >
 > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
 > >
 > >
 > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
 > >> Dear gmx users,
 > >>
 > >> I want to simulate a peptide in water. The peptide has a formyl residue 
as the
 > >> N-terminus. I got the parameters of it and then add it to the .rtp file of
 > >> charmm36.ff as below:
 > >>
 > >> [ For ]
 > >> [ atoms ]
 > >> ; name type charge chargegroup
 > >> C C 0.4500 0
 > >> O O -0.5700 0
 > >> [ bonds ]
 > >> ; ai aj fu b0 kb, b0 kb
 > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
 > >>
 > >> [ pairs ]
 > >> ; ai aj fu
 > >>
 > >> [ angles ]
 > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
 > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
 > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
 > >>
 > >> [ dihedrals ]
 > >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
 > >>
 > >> But when I do what I described, I face this fatal error:
 > >> Fatal error:
 > >> No atoms found in .rtp file in residue pairs
 > >>
 > >> Would you help me with this problem? Did I add the formyl in a wrong way?
 > >>
 > >
 > > Your [pairs] directive is empty, hence the error. Your [dihedrals] 
directive
 > > will also produce the same error. There are no possible pairs in a unit
 > > containing so few atoms, so you don't even need this. You may need to 
define
 > > dihedrals, however, but they also depend upon the next residue.
 > >
 > > You also have several other mistakes:
 > 

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Shima Arasteh]

Even in gromos87, if I want to make a .rtp file for formyl, I need to put H 
atom in it? I mean, defining all atoms of a residue is necessary? Aren't the 
hydrogen atoms set by the gromacs package?

Cheers,
Shima




 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Sunday, May 13, 2012 8:36 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs
 


On 5/13/12 11:43 AM, Shima Arasteh wrote:
> Again thanks for all your replies.
> As I got through your advices, I found that the atoms contribute in making 
> bonds
> and angles in a residue , or make dihedrals in a residue ( or with atoms in 
> next
> ones) plus the charge of a the residue should be defined properly in .rtp 
> files
> to define the new residue in aminoacid.rtp file of CHARMM36 force field.
> So I arranged this lines to define formyl in .rtp file. And I got the 
> topology.
> But there are some questions for me here:
>
> 1. How can I be sure the formyl which I defined is correct? Is getting the
> topology is enough to be sure of the correct output?
>

It is incorrect.  As I said before, a formyl group is an aldehyde and has an H 
atom attached to C, e.g. -CH(=O).  At present, you are defining a -C=O group 
with an incomplete carbon valence.

http://en.wikipedia.org/wiki/Aldehyde

> The .rtp file for formyl is as below:
> [ For ]
> [ atoms ]
> ; name type charge chargegroup
> C CTL1 0.5700 0
> O O -0.5700 0
> [angles ]
> ai aj ak
> O C +N
> [ bonds ]
> C O
> C +N
>
> [ dihedrals ]
> O C +N +CA
>

Aside from the missing atom (and resulting missing bonds, angles, and 
dihedral), 
the format of this entry is OK.

> 2. There are lots of numbers in .itp file which I got through the swissparam.
> But I think the charge of atoms may be useful in this file and also I can just
> find the atoms contribute in bonds and angles and . Am I right? Or I may 
> get
> some other useful information which I can get through the files of swissparam?
>

If the existing bonded parameters for each interaction type (in ffbonded.itp) 
are sufficient for defining these interactions, then you can omit the content 
of 
the .itp file you've been using in the .rtp entry and rely on the force field 
to 
look up those values.  There may be some interactions that are not in agreement 
(or do not exist), in which case you need to either define these parameters in 
the .rtp entry itself or in ffbonded.itp so that they will be detected by 
grompp 
later.

-Justin

> Thanks in advance, and sorry for disturbing you friends.
> Shima
>
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Saturday, May 12, 2012 10:12 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in 
> residue pairs
>
>
>
> On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>  >
>  >
>  > On 5/12/12 1:32 PM, Shima Arasteh wrote:
>  >> Dear gmx users,
>  >>
>  >> I want to simulate a peptide in water. The peptide has a formyl residue 
>as the
>  >> N-terminus. I got the parameters of it and then add it to the .rtp file of
>  >> charmm36.ff as below:
>  >>
>  >> [ For ]
>  >> [ atoms ]
>  >> ; name type charge chargegroup
>  >> C C 0.4500 0
>  >> O O -0.5700 0
>  >> [ bonds ]
>  >> ; ai aj fu b0 kb, b0 kb
>  >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>  >>
>  >> [ pairs ]
>  >> ; ai aj fu
>  >>
>  >> [ angles ]
>  >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>  >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>  >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>  >>
>  >> [ dihedrals ]
>  >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>  >>
>  >> But when I do what I described, I face this fatal error:
>  >> Fatal error:
>  >> No atoms found in .rtp file in residue pairs
>  >>
>  >> Would you help me with this problem? Did I add the formyl in a wrong way?
>  >>
>  >
>  > Your [pairs] directive is empty, hence the error. Your [dihedrals] 
>directive
>  > will also produce the same error. There are no possible pairs in a unit
>  > containing so few atoms, so you don't even need this. You may need to 
>define
>  > dihedrals, however, but they also depend upon the next residue.
>  >
>  > You also have several other mistakes:
>  >
>  > 1. A formyl group has a proton on it; yours has none
>  > 2. Your net charge on the formyl group is not zero, though this may or may 
>not
>  > be a consequence of point #1
>  > 3. There is no connectivity information for linking to the next residue, 
>which
>  > will mean the formyl group will not be chemically bonded. This also 
>affects your
>  > dihedrals.
>  >
>
> Another that I just caught as I hit send:
>
> 4. In your [bonds] and [angles] directives, you use atom numbers - they should
> be names
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu 

[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

[Sangita Kachhap]

Hello all

I am running GROMACS Tutorial: KALP15 in POPC
I have compeleted production run 1 ns now I want to extend it for next 1 ns.
For this I have used commond:

tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt

I am getting files are:
ener.edr
md.log
state.cpt
state_prev.cpt
traj.trr
traj.xtc
confout.gro

During first 1 ns production I have got all files with prefix  md_0_1.
How I can get it (prefix md_0_2. for all the above files)in next 1 ns production
run.

Anyone please suggest.


With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH

__
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Shima Arasteh]

OK, so I entered the H atom corresponding to the structure and then changed the 
file as below,

[ For ]
 [ atoms ]
;  name    type charge   charge group
    C   CTL1 0.5700   0
    O   O   -0.5700   0
    H   HC   0.00 0

 [angles ]
  ai    aj    ak   
  O C +N 
  O C  H

 [ bonds ]
 C  O    
 C +N
 C  H
 
 [ dihedrals ]
  O C   +N   +CA 
  H C   +N   +H






 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Sunday, May 13, 2012 8:36 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs
 


On 5/13/12 11:43 AM, Shima Arasteh wrote:
> Again thanks for all your replies.
> As I got through your advices, I found that the atoms contribute in making 
> bonds
> and angles in a residue , or make dihedrals in a residue ( or with atoms in 
> next
> ones) plus the charge of a the residue should be defined properly in .rtp 
> files
> to define the new residue in aminoacid.rtp file of CHARMM36 force field.
> So I arranged this lines to define formyl in .rtp file. And I got the 
> topology.
> But there are some questions for me here:
>
> 1. How can I be sure the formyl which I defined is correct? Is getting the
> topology is enough to be sure of the correct output?
>

It is incorrect.  As I said before, a formyl group is an aldehyde and has an H 
atom attached to C, e.g. -CH(=O).  At present, you are defining a -C=O group 
with an incomplete carbon valence.

http://en.wikipedia.org/wiki/Aldehyde

> The .rtp file for formyl is as below:
> [ For ]
> [ atoms ]
> ; name type charge chargegroup
> C CTL1 0.5700 0
> O O -0.5700 0
> [angles ]
> ai aj ak
> O C +N
> [ bonds ]
> C O
> C +N
>
> [ dihedrals ]
> O C +N +CA
>

Aside from the missing atom (and resulting missing bonds, angles, and 
dihedral), 
the format of this entry is OK.

> 2. There are lots of numbers in .itp file which I got through the swissparam.
> But I think the charge of atoms may be useful in this file and also I can just
> find the atoms contribute in bonds and angles and . Am I right? Or I may 
> get
> some other useful information which I can get through the files of swissparam?
>

If the existing bonded parameters for each interaction type (in ffbonded.itp) 
are sufficient for defining these interactions, then you can omit the content 
of 
the .itp file you've been using in the .rtp entry and rely on the force field 
to 
look up those values.  There may be some interactions that are not in agreement 
(or do not exist), in which case you need to either define these parameters in 
the .rtp entry itself or in ffbonded.itp so that they will be detected by 
grompp 
later.

-Justin

> Thanks in advance, and sorry for disturbing you friends.
> Shima
>
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Saturday, May 12, 2012 10:12 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in 
> residue pairs
>
>
>
> On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>  >
>  >
>  > On 5/12/12 1:32 PM, Shima Arasteh wrote:
>  >> Dear gmx users,
>  >>
>  >> I want to simulate a peptide in water. The peptide has a formyl residue 
>as the
>  >> N-terminus. I got the parameters of it and then add it to the .rtp file of
>  >> charmm36.ff as below:
>  >>
>  >> [ For ]
>  >> [ atoms ]
>  >> ; name type charge chargegroup
>  >> C C 0.4500 0
>  >> O O -0.5700 0
>  >> [ bonds ]
>  >> ; ai aj fu b0 kb, b0 kb
>  >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>  >>
>  >> [ pairs ]
>  >> ; ai aj fu
>  >>
>  >> [ angles ]
>  >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>  >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>  >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>  >>
>  >> [ dihedrals ]
>  >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>  >>
>  >> But when I do what I described, I face this fatal error:
>  >> Fatal error:
>  >> No atoms found in .rtp file in residue pairs
>  >>
>  >> Would you help me with this problem? Did I add the formyl in a wrong way?
>  >>
>  >
>  > Your [pairs] directive is empty, hence the error. Your [dihedrals] 
>directive
>  > will also produce the same error. There are no possible pairs in a unit
>  > containing so few atoms, so you don't even need this. You may need to 
>define
>  > dihedrals, however, but they also depend upon the next residue.
>  >
>  > You also have several other mistakes:
>  >
>  > 1. A formyl group has a proton on it; yours has none
>  > 2. Your net charge on the formyl group is not zero, though this may or may 
>not
>  > be a consequence of point #1
>  > 3. There is no connectivity information for linking to the next residue, 
>which
>  > will mean the formyl group will not be chemically bonded. This also 
>affects your
>  > dihedrals.
>  >
>
> Another that I just caught as I hit send:
>
> 4. In your [bonds] and

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Justin A. Lemkul]

On 5/13/12 11:43 AM, Shima Arasteh wrote:

Again thanks for all your replies.
As I got through your advices, I found that the atoms contribute in making bonds
and angles in a residue , or make dihedrals in a residue ( or with atoms in next
ones) plus the charge of a the residue should be defined properly in .rtp files
to define the new residue in aminoacid.rtp file of CHARMM36 force field.
So I arranged this lines to define formyl in .rtp file. And I got the topology.
But there are some questions for me here:

1. How can I be sure the formyl which I defined is correct? Is getting the
topology is enough to be sure of the correct output?



It is incorrect.  As I said before, a formyl group is an aldehyde and has an H 
atom attached to C, e.g. -CH(=O).  At present, you are defining a -C=O group 
with an incomplete carbon valence.


http://en.wikipedia.org/wiki/Aldehyde


The .rtp file for formyl is as below:
[ For ]
[ atoms ]
; name type charge chargegroup
C CTL1 0.5700 0
O O -0.5700 0
[angles ]
ai aj ak
O C +N
[ bonds ]
C O
C +N

[ dihedrals ]
O C +N +CA



Aside from the missing atom (and resulting missing bonds, angles, and dihedral), 
the format of this entry is OK.



2. There are lots of numbers in .itp file which I got through the swissparam.
But I think the charge of atoms may be useful in this file and also I can just
find the atoms contribute in bonds and angles and . Am I right? Or I may get
some other useful information which I can get through the files of swissparam?



If the existing bonded parameters for each interaction type (in ffbonded.itp) 
are sufficient for defining these interactions, then you can omit the content of 
the .itp file you've been using in the .rtp entry and rely on the force field to 
look up those values.  There may be some interactions that are not in agreement 
(or do not exist), in which case you need to either define these parameters in 
the .rtp entry itself or in ffbonded.itp so that they will be detected by grompp 
later.


-Justin


Thanks in advance, and sorry for disturbing you friends.
Shima


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, May 12, 2012 10:12 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs



On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
 >
 >
 > On 5/12/12 1:32 PM, Shima Arasteh wrote:
 >> Dear gmx users,
 >>
 >> I want to simulate a peptide in water. The peptide has a formyl residue as 
the
 >> N-terminus. I got the parameters of it and then add it to the .rtp file of
 >> charmm36.ff as below:
 >>
 >> [ For ]
 >> [ atoms ]
 >> ; name type charge chargegroup
 >> C C 0.4500 0
 >> O O -0.5700 0
 >> [ bonds ]
 >> ; ai aj fu b0 kb, b0 kb
 >> 1 2 1 0.12220 779866.6 0.12220 779866.6
 >>
 >> [ pairs ]
 >> ; ai aj fu
 >>
 >> [ angles ]
 >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
 >> 2 1 3 1 123.4390 403.48 123.4390 403.48
 >> 2 1 4 1 123.4390 403.48 123.4390 403.48
 >>
 >> [ dihedrals ]
 >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
 >>
 >> But when I do what I described, I face this fatal error:
 >> Fatal error:
 >> No atoms found in .rtp file in residue pairs
 >>
 >> Would you help me with this problem? Did I add the formyl in a wrong way?
 >>
 >
 > Your [pairs] directive is empty, hence the error. Your [dihedrals] directive
 > will also produce the same error. There are no possible pairs in a unit
 > containing so few atoms, so you don't even need this. You may need to define
 > dihedrals, however, but they also depend upon the next residue.
 >
 > You also have several other mistakes:
 >
 > 1. A formyl group has a proton on it; yours has none
 > 2. Your net charge on the formyl group is not zero, though this may or may 
not
 > be a consequence of point #1
 > 3. There is no connectivity information for linking to the next residue, 
which
 > will mean the formyl group will not be chemically bonded. This also affects 
your
 > dihedrals.
 >

Another that I just caught as I hit send:

4. In your [bonds] and [angles] directives, you use atom numbers - they should
be names

-Justin

--


Justin A. Lemkul, Ph.D.
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.
Department of Bioc

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Shima Arasteh]

Again thanks for all your  replies.
As I got through your advices, I found that the atoms contribute in making 
bonds and angles in a residue , or make dihedrals in a residue ( or with atoms 
in next ones) plus the charge of a the residue should be defined properly in 
.rtp files to define the new residue in aminoacid.rtp file of CHARMM36 force 
field.
So I arranged this lines to define formyl in .rtp file. And I got the topology. 
But there are some questions for me here:

1. How can I be sure the formyl which I defined is correct? Is getting the 
topology is enough to be sure of the correct output?


The .rtp file for formyl is as below:
[ For ]
 [ atoms ]
;  name    type charge   chargegroup
    C   CTL1 0.5700   0
    O   O   -0.5700   0
 [angles ]
  ai    aj    ak   
  O C +N 
 [ bonds ]
 C  O    
 C +N
 
 [ dihedrals ]
  O C   +N   +CA


2. There are lots of numbers in .itp file which I got through the swissparam.  
But  I think the charge of atoms may be useful in this file and also I can just 
find the atoms contribute in bonds and angles and . Am I right? Or I may 
get some other useful information which I can get through the files of 
swissparam?

Thanks in advance, and sorry for disturbing you friends.

Shima




 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Saturday, May 12, 2012 10:12 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue 
pairs
 


On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>
>
> On 5/12/12 1:32 PM, Shima Arasteh wrote:
>> Dear gmx users,
>>
>> I want to simulate a peptide in water. The peptide has a formyl residue as 
>> the
>> N-terminus. I got the parameters of it and then add it to the .rtp file of
>> charmm36.ff as below:
>>
>> [ For ]
>> [ atoms ]
>> ; name type charge chargegroup
>> C C 0.4500 0
>> O O -0.5700 0
>> [ bonds ]
>> ; ai aj fu b0 kb, b0 kb
>> 1 2 1 0.12220 779866.6 0.12220 779866.6
>>
>> [ pairs ]
>> ; ai aj fu
>>
>> [ angles ]
>> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>> 2 1 3 1 123.4390 403.48 123.4390 403.48
>> 2 1 4 1 123.4390 403.48 123.4390 403.48
>>
>> [ dihedrals ]
>> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>>
>> But when I do what I described, I face this fatal error:
>> Fatal error:
>> No atoms found in .rtp file in residue pairs
>>
>> Would you help me with this problem? Did I add the formyl in a wrong way?
>>
>
> Your [pairs] directive is empty, hence the error. Your [dihedrals] directive
> will also produce the same error. There are no possible pairs in a unit
> containing so few atoms, so you don't even need this. You may need to define
> dihedrals, however, but they also depend upon the next residue.
>
> You also have several other mistakes:
>
> 1. A formyl group has a proton on it; yours has none
> 2. Your net charge on the formyl group is not zero, though this may or may not
> be a consequence of point #1
> 3. There is no connectivity information for linking to the next residue, which
> will mean the formyl group will not be chemically bonded. This also affects 
> your
> dihedrals.
>

Another that I just caught as I hit send:

4. In your [bonds] and [angles] directives, you use atom numbers - they should 
be names

-Justin

-- 


Justin A. Lemkul, Ph.D.
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] dipole moment

[dina dusti]

Dear Justin,

Thank you very much from your response.

Best Regards
Dina




 From: Justin A. Lemkul 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Sunday, May 13, 2012 5:23 PM
Subject: Re: [gmx-users] dipole moment
 


On 5/13/12 8:41 AM, dina dusti wrote:
> Dear GROMACS Specialists,
> 
> I have one system consists of water and two other molecules. I work by MARTINI
> CG force field. I want to calculate dipole moment of molecules in water.
> May I ask you to help me, Please?
> 

I doubt you can.  Unless you are using version 2.P of the force field (which 
contains polarizable water), MARTINI uses a single, uncharged particle to 
represent water.  If there are no charges, there is no dipole.

-Justin

-- 

Justin A. Lemkul, Ph.D.
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] dipole moment

[Justin A. Lemkul]

On 5/13/12 8:41 AM, dina dusti wrote:

Dear GROMACS Specialists,

I have one system consists of water and two other molecules. I work by MARTINI
CG force field. I want to calculate dipole moment of molecules in water.
May I ask you to help me, Please?



I doubt you can.  Unless you are using version 2.P of the force field (which 
contains polarizable water), MARTINI uses a single, uncharged particle to 
represent water.  If there are no charges, there is no dipole.


-Justin

--


Justin A. Lemkul, Ph.D.
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] *.ITP file

[Justin A. Lemkul]

On 5/13/12 5:54 AM, Kowsar Bagherzadeh wrote:

Dear Users,
I am trying to generate an *.ITP file for a ligand I am studying using Prodrg
server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar
hydrogens) while the *.ITP file dispays 37 atoms and it does not display the
double bond in the structure, which results in an error in simulation. Other
files that Prodrg gives like DRGAPH.PDB display 37 atoms same as the *.ITP file
and they also do not display the double bond in the structure ! only the
DRGFIN.PDB with 41 atoms ( all hydrogens) displays the double bond. I have used
Prodrg several times before and this is the first time it happens. are there any
other online services or any software for the purpose? Thank you



Whether or not any file "displays" a double bond is irrelevant.  There will not 
be duplicate bonds in the .itp file, nor will a double bond necessarily appear 
in visualization software, though some programs may try to guess.


The most important things to do are obtain the coordinate file that matches the 
topology (e.g., the one that does not have nonpolar hydrogens, per Gromos 
convention) and realize that you will need to do a fair bit of work to improve 
the PRODRG topology: http://pubs.acs.org/doi/abs/10.1021/ci100335w


ATB is another option.  It is newer and performs better.

http://compbio.biosci.uq.edu.au/atb/

-Justin

--


Justin A. Lemkul, Ph.D.
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] dipole moment

[dina dusti]

Dear GROMACS Specialists,

I have one system consists of water and two other molecules. I work by MARTINI 
CG force field. I want to calculate dipole moment of molecules in water.
May I ask you to help me, Please?

Best Regards
Dina
-- 
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[gmx-users] *.ITP file

[Kowsar Bagherzadeh]

 Dear Users,
 I am trying to generate an *.ITP file for a ligand I am studying using Prodrg 
server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar 
hydrogens) while the *.ITP file dispays 37 atoms and it does not display the 
double bond in the structure, which results in an error in simulation. Other 
files that Prodrg gives like DRGAPH.PDB display 37 atoms same as the *.ITP file 
and they also do not display the double bond in the structure ! only the 
DRGFIN.PDB with 41 atoms ( all hydrogens) displays the double bond. I have used 
Prodrg several times before and this is the first time it happens. are there 
any other online services or any software for the purpose? Thank you-- 
gmx-users mailing listgmx-users@gromacs.org
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