[gmx-users] gromacs
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 14 21:47:56 CEST 2008
He, Yang wrote:
> Hello,
>
> This is my content in the *nb.itp
>
> [ atomtypes ]
> ;name mass charge ptype c6 c12
> Ab 134.1 0.683 A 0.0 0.0
> P1 94.97 -0.276 A 0.0 0.0
> Tb 125.1 -0.683 A 0.0 0.0
> P2 94.97 -0.622 A 0.0 0.0
> S1 83.11 -0.622 A 0.0 0.0
> S3 83.11 0.346 A 0.0 0.0
> S2 83.11 0.346 A 0.0 0.0
> S4 83.11 0.276 A 0.0 0.0
>
>
> [ nonbond_params ]
> ; i j func c6 c12
> Ab P1 1 1.075559 0.265854
> Tb P2 1 0.540666 0.067179
> S1 S3 1 0.117973 0.003198
> S2 S4 1 0.117973 0.003198
>
>
>
>
> [ pairtypes ]
> ; i j func cs10 cs12
> Ab Tb 1 1.099147E-6 7.704251E-6
>
> in this file , I just defined the atoms for DNA. So how I can solve this problem .I really got confused.
>
You need to include parameters for OW and the interactions of OW with the other
atom types.
-Justin
> Thank you for your guidence.
>
> Regards,
>
> Yang
> ________________________________________
> From: Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, October 14, 2008 12:23 PM
> To: He, Yang; Gromacs Users' List
> Subject: Re: [gmx-users] gromacs
>
> 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
>> #endif
>> #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
>> #else
>> 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
>> #endif
>> #endif
>> #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
>> #endif
>>
>> #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
>> #endif
>>
>> 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.
>
> -Justin
>
>> Thank you for your favor.
>>
>> Regards,
>>
>> Yang
>>
>> ________________________________________
>> 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.
>>
>> -Justin
>>
>>> Thank you in advance.
>>>
>>> Yang
>>> _______________________________________________
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>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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