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

[Olga Ivchenko]

Dear All,

I just want to know if the programm PRODRG is able to generate for my ligand
files with .top extension.

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>

>
>
> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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