Hello Gmx Usrs, I am new to Gromacs. I am trying to simulate a protein-membrane complex using berger-oplsaa combination . I have created a topology file for the protein using pdb2gmx in order to then build up the topology for my system using the include file mechanism. After that I tried to use my system.top in grompp ( grompp -f xx.mdp -c system.pdb -p system.top -o out.tpr ) but I get a warning about atoms in top and pdb does not match. I went trough the mailing list but I have still doubt. I checked where were the differences. It seems that the order of the aromatic ring in the pdb and in the top didn't match.
To be clear (tyr as example but the same problem occur with his): .pdb .top N N HN H CA CA HA HA CB CB HB1 HB1 HB2 HB2 CG CG CD1 CD1 HD1 HD1 CE1 CD2 HE1 HD2 CZ CE1 OH HE1 HH CE2 CD2 HE2 HD2 CZ CE2 OH HE2 HH C C O O Is this because the .top seems follow the order presents in the rtp file that I have (am I right?). Assuming that this is the case I am wondering if changing the atoms order in the rtp from: [ TYR ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_149 -0.005 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_145 -0.115 3 CD1 opls_145 -0.115 4 HD1 opls_146 0.115 4 CD2 opls_145 -0.115 5 HD2 opls_146 0.115 5 CE1 opls_145 -0.115 6 HE1 opls_146 0.115 6 CE2 opls_145 -0.115 7 HE2 opls_146 0.115 7 CZ opls_166 0.150 8 OH opls_167 -0.585 8 HH opls_168 0.435 8 C opls_235 0.500 9 O opls_236 -0.500 9 to: [ TYR ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_149 -0.005 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_145 -0.115 3 CD1 opls_145 -0.115 4 HD1 opls_146 0.115 4 CE1 opls_145 -0.115 6 HE1 opls_146 0.115 6 CZ opls_166 0.150 8 OH opls_167 -0.585 8 HH opls_168 0.435 8 CE2 opls_145 -0.115 7 HE2 opls_146 0.115 7 CD2 opls_145 -0.115 5 HD2 opls_146 0.115 5 C opls_235 0.500 9 O opls_236 -0.500 9 can that have a further effect since it seems that the file handling is based on line position and not atoms name. Any suggestions are welcome Thanks Irene -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
