[gmx-users] gromacs

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
> #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

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