Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 14 21:23:44 CEST 2008
He, Yang wrote:
> Hello Justin,
> Thank you for your reply. I am using the gromacs to simulate a case about the course grain for DNA. This case includes some superatoms in the course grain force field and I have defined the superatoms in the .atp files and the atoms type in the water like this:
> Ab 134.1; Adenine base of DNA
> Tb 125.1; Thymine base of DNA
> S 83.11; Sugar of DNA
> P 94.97; Phosphate of DNA
> OW 15.99940; water oxygen in SOL
> HW 1.00800; water hydrogen in SOL
> But it shows that Fatal error:
> Atomtype 'OW' not found!
> Also, this is my spc.itp file
> [ moleculetype ]
> ; molname nrexcl
> SOL 3
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> #ifdef _FF_GROMACS
> 1 OW 1 SOL OW 1 -0.82
> 2 HW 1 SOL HW1 1 0.41
> 3 HW 1 SOL HW2 1 0.41
> #ifdef _FF_GROMOS96
> #ifdef HEAVY_H
> 1 OW 1 SOL OW 1 -0.82 9.95140
> 2 H 1 SOL HW1 1 0.41 4.03200
> 3 H 1 SOL HW2 1 0.41 4.03200
> 1 OW 1 SOL OW 1 -0.82 15.99940
> 2 H 1 SOL HW1 1 0.41 1.00800
> 3 H 1 SOL HW2 1 0.41 1.00800
> #ifdef _FF_OPLS
> 1 opls_116 1 SOL OW 1 -0.82
> 2 opls_117 1 SOL HW1 1 0.41
> 3 opls_117 1 SOL HW2 1 0.41
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j funct length force.c.
> 1 2 1 0.1 345000 0.1 345000
> 1 3 1 0.1 345000 0.1 345000
> [ angles ]
> ; i j k funct angle force.c.
> 2 1 3 1 109.47 383 109.47 383
> [ exclusions ]
> 1 2 3
> 2 1 3
> 3 1 2
> Can you help me solve this problem
Well, what's in your *nb.itp file? You're obviously not using any of the force
fields that are called in the spc.itp file, so grompp doesn't know how to treat
OW in your force field.
> Thank you for your favor.
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, October 14, 2008 12:01 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] gromacs
> He, Yang wrote:
>> Hi all users,
>> I juse encountered a problem when I run the code about the course grain for DNA,
>> it shows like this
>> creating statusfile for 1 node...
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>> checking input for internal consistency...
>> calling cpp...
>> In file included from ffyxh.itp:8,
>> from hust.top:11:
>> ffyxhnb.itp:25:61: warning: no newline at end of file
>> In file included from ffyxh.itp:9,
>> from hust.top:11:
>> ffyxhbon.itp:26:5: warning: no newline at end of file
>> In file included from hust.top:65:
>> ffyxh.atp:6:34: warning: no newline at end of file
>> hust.top:76:17: warning: no newline at end of file
>> processing topology...
>> Generated 32 of the 36 non-bonded parameter combinations
>> Program grompp, VERSION 3.3.1
>> Source code file: toputil.c, line: 61
>> Fatal error:
>> Atomtype 'OW' not found!
>> I have tried to solve that , but it did not still work . So anyone of you can tell me how to solve that.
> Well, what have you done to solve it? From the messages grompp is printing out,
> it looks like the format of your files is badly mangled. You're calling
> parameters for an atomtype which does not exist within the force field you've
> apparently created. Parameters need to be defined within the .atp, *bon.itp,
> and *nb.itp files for it to be recognized.
>> Thank you in advance.
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users