[gmx-users] Re: Gromacs error

[Mark Abraham]

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