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

[Justin A. Lemkul]

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
> 
> 
> 
> 

-- 
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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

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