Dear Sir, thank you so much for your reply. I made the index.ndx file and ran grompp with the index file that I have made, but with no change and I still get the same mesg. I just hope I have understood your suggestion correctly. Which manual sorting are we talking about? What exactly is the problem?
thanks and regards, Pri... --- David van der Spoel <[EMAIL PROTECTED]> wrote: > priyanka srivastava wrote: > > 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 > > > you should probably sort the coordinates of the > lipids to match that in > the topology file. you can do that by generating an > index file (manually > or with a script that you write). > > > > > > > > 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 > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > 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 > __________________________________________________ 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
