[gmx-users] Re: Gromacs error

[bharat gupta]

I took all the parameters of Ptyr from amber parameter database and followed
what was said in the documentation. Shall mail the changes made for topology

On Fri, Jun 17, 2011 at 5:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 06/17/2011 12:18 PM, bharat gupta wrote:
>
>> thanks..  I fixed the problem by using the command execstack -c filename
>>
>>
>> but I have another issue .. I am am preparing the structure for simulation
>> which is a docked complex containing Phospharylated tyrosine. I am using
>> Amber 99 force field and update the residuetypes.dat, aminoacid.rtp,
>> ffbonded.itp files for pTYR but still the error that "Residue 'PTYR' not
>> found in residue topology database" ... but all the changes I have made then
>> where else could the problem be ??
>>
>
> Isn't it rather more likely your error is in something you've already done?
> Be sure you have followed http://www.gromacs.org/**
> Documentation/How-tos/Adding_**a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>
>
> Mark
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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