[gmx-users] Re: which force file has parameters for creatine md simulations?

[Justin A. Lemkul]

Olga Ivchenko wrote:
> Dear All,
> 
> I just want to know if the programm PRODRG is able to generate for my 
> ligand files with .top extension.
> 

No, but it is trivial to interconvert .itp and .top manually:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

-Justin

> I have two files one is itp format and other is gro using PRODRG.
> If it is possible what is the name here 
> :http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta#DRGFIN.GRO
> 
> Yours sincerely,
> Olga
> 
> 2010/11/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     Olga Ivchenko wrote:
> 
>         Dear All,
> 
>         I have created creating topology file using  *prodrg_beta (using
>         gromos 96 ff)
>         <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta>*. When I
>         am trying to run energy minimization it writes an error:
> 
> 
>     Please consider carefully the caveats about PRODRG noted here
>     (second paragraph):
> 
>     http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
> 
> 
>         Syntax error - File creatine.top, line 19
>         Last line read:
>         '[ moleculetype ]'
>         Invalid order for directive moleculetype
> 
>         I looked at previoust mailing lists according this problem. I
>         can not find direct answer.
> 
> 
>     http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults
> 
>     Somehow you've cut and pasted such that you've got a [moleculetype]
>     directive out of order.
> 
> 
>         I tried to add this line in the topology file
> 
>         #include "ffG43a1.ff/DRGGMX.itp"
> 
>         An again an error:Fatal error:
>         Topology include file "ffG43a1.ff/DRGGMX.itp" not found
> 
> 
>     Then either the file doesn't exist or isn't within the search path
>     grompp is trying.
> 
>     -Justin
> 
> 
> 
>         Please can you advice me on this.
> 
> 
>         Yours sincerely,
> 
>         Olga
> 
> 
> 
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================