[gmx-users] Re: Gromacs error

[Mark Abraham]

On 06/17/2011 06:36 PM, bharat gupta wrote:
> I took all the parameters of Ptyr from amber parameter database and 
> followed what was said in the documentation.

The fact that you seem to change the capitalization of "PTYR" every time 
you type it does not inspire confidence that you've taken due care of 
all the details required.

> Shall mail the changes made for topology

I don't have time to sift through them. Try using the diff tool to 
compare before and after so that you can verify that your mental picture 
of what you have done agrees with what you have done.

Mark

> On Fri, Jun 17, 2011 at 5:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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
>
>     Mark
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>
> -- 
> Bharat
> Ph.D. Candidate
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