Thanks again for your kind response. I guess I will write down my problem once again :-)
I am trying to study a pure bilayer system for which I am interested in running the production run using gromacs. I already have the system with me i.e. a pdb file after the minimization and all the constraints etc. Now what I am intersted in doing is, I want to run the production run ONLY using gromacs. So, My starting point is a pdb file containing only the DMPC residues. The steps that I am following are as follows: 1. Generate a .top file from the information available on Peter Tielemann's website i.e. by using lipid.itp, dmpc.itp. The identifier used for water is SOL though the water present in my original pdb file is TIP3. 2. I am unable to use pdb2gmx since it gives me the error: "residue DMPC is not present in residue topology database" 3. So, I use editconf to make the .gro file 4. Then I am adding the box-dimensions using editconf once again. 5. Now when I run grompp after this using the .top file that I have made (from the website) and the .gro (from editconf) I get the following mesg: calling /lib/cpp... processing topology... Generated 1369 of the 2211 non-bonded parameter combinations Excluding 3 bonded neighbours for DMPC 96 Excluding 2 bonded neighbours for SOL 2866 processing coordinates... Warning: atom names in 96_neatsys14.top and test.gro don't match (CN1 - NC3) Warning: atom names in 96_neatsys14.top and test.gro don't match (CN2 - C13) Warning: atom names in 96_neatsys14.top and test.gro don't match (CN3 - C14) Warning: atom names in 96_neatsys14.top and test.gro don't match (NTM - C15) Warning: atom names in 96_neatsys14.top and test.gro don't match (CA - C12) Warning: atom names in 96_neatsys14.top and test.gro don't match (CB - C11) Warning: atom names in 96_neatsys14.top and test.gro don't match (OA - PO4) Warning: atom names in 96_neatsys14.top and test.gro don't match (P - O13) Warning: atom names in 96_neatsys14.top and test.gro don't match (OB - O14) Warning: atom names in 96_neatsys14.top and test.gro don't match (OC - O11) Warning: atom names in 96_neatsys14.top and test.gro don't match (OD - O12) Warning: atom names in 96_neatsys14.top and test.gro don't match (CC - C1) Warning: atom names in 96_neatsys14.top and test.gro don't match (CD - C2) Warning: atom names in 96_neatsys14.top and test.gro don't match (OE - O21) Warning: atom names in 96_neatsys14.top and test.gro don't match (C2A - C21) Warning: atom names in 96_neatsys14.top and test.gro don't match (OF - O22) Warning: atom names in 96_neatsys14.top and test.gro don't match (C2B - C22) Warning: atom names in 96_neatsys14.top and test.gro don't match (C2C - C3) Warning: atom names in 96_neatsys14.top and test.gro don't match (C2D - O31) Warning: atom names in 96_neatsys14.top and test.gro don't match (C2E - C31) (more than 20 non-matching atom names) WARNING 1 [file "96_neatsys14.top", line 20]: 13014 non-matching atom names atom names from 96_neatsys14.top will be used atom names from test.gro will be ignored When I look at the atom types that are there in the .gro file they seem to be the problem, i.e. the choline Nitrogen is represented as N only which refers to a peptide N in gromacs. What should I do? Please help me and also suggest me if I am going in the right direction or not? eagerly waiting for the gromacs experts response, warm regards, Pri... __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
