Hi nikhil damle When running pdb2bmx for ATP in a PDB file using the ffG43a1, shows warnings because atom names don't match. You have to cut the ATP coordinates out to other PDB file, to convert it to gromacs format (.gro) using editconf and edit this file in gromacs format to match the atom namings in the rtp file. Then, one can run pdb2gmx to that file in gromacs format to generate the topology for the ATP. When you have gotten this topology file, you can change its extension to ITP. By other side you need to run pdb2gmx for the rest of the molecule. Then you can merge the .gro files and the topology files, as explained in the GROMACS Tutorial for Drug-Enzyme Complex (http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf). Lucio PhD. Student Lab. Dr. Federico Sanchez Instituto de Biotecnologia, UNAM Mexico
El lun, 22-06-2009 a las 10:09 +0530, nikhil damle escribió: > Hi all, > > I want to carry out a MD simulation of a receptor protein in > presence of ATP molecule. ATP is included in .rtp file of ffG43a1 > force field. but post pdb2gmx, .pdb output file does not show crds of > ATP. Does it mean that ATP is not recognized as a residue of protein > in spite of being included in .rtp file. If so how does one carry out > this simulation ? If .itp file of ATP is an option, how can one get > the specific values of charges etc for constructing .itp file. Manual > does not mention anything regarding it. > > Please help as soon as possible. > > Regards, > Nikhil > > > > ______________________________________________________________________ > Love Cricket? Check out live scores, photos, video highlights and > more. Click here. > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
