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.abra...@anu.edu.au <mailto:mark.abra...@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-- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
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