Hi Prasun, As a side-note to the replies of Justin and Florian, why not take the following approach?:
1. run pdb2gmx on the monomer, giving structure and topology for one unit (2. energy minimize in vacuum) 3. use editconf to make a transformed copy of the monomer -- now, you know for sure that both are topologically identical -- 4. concatenate the two chains; if it's pdb format just grep all ATOM records from both files into a new file 5. modify Protein 1 to Protein 2 under [ molecules ] in the topology 6. setup a box and solvate and continue as usual Hope it helps, Tsjerk On Thu, Jul 31, 2008 at 2:24 PM, Florian Haberl <[EMAIL PROTECTED]> wrote: > Hi, > > On Thursday, 31. July 2008, prasun kumar wrote: >> Dear user, >> I want to check the dimerization of a peptide chain having 227 residues.I >> am doing the following steps: >> >> 1. First i transformed the given peptide by 20 angstrom by >> modifying corresponding pdb file and save it as >> f1.pdb(say),original file given was 'f.pdb'(say) >> >> 2 .Now i run the pdb2gmx command for both the proteins. >> >> 3 add the two files and remove the END of one of the file(i >> mean to say i remove the END from the middle). >> >> 4. Now run the EDITCONF command >> >> 5 Modify the topology file in the molecules section by >> replacing 1 by2. >> >> 6 run the grompp command and mdrun for energy >> minimization for 2000 steps. >> >> 7 again run grompp for positional restrained dynamics >> >> till here every thing work >> >> but when i tried to run mdrun its telling your protein is not minimizd >> properly. >> >> after this I tried another method by modifying opology file in the >> following way >> >> I added one proteins topology file in the another one by adding line >> INCLUDE f1_top1.top(topology file name) >> >> again its working till grompp(pr) >> now when i am trying to run mdrun its givin following error >> >> Found a second defaults directive, file >> "/usr/share/gromacs/top/ffG43a1.itp", line 6 >> >> What to do? >> >> I am not getting any other way.Please help me. >> >> Thanx in advance >> Regards >> >> PRASUN (ASHOKA) > > Have you checked your structure (missing residues and so on ..), can you > simulate one monomer without problems? > > In principle it should work with the first approach, but it is. (often) > neccessary to start the simulation with position restraints to get a valid > structure for a free MD simulation. > > See the wiki for the normal simulation protocol ( > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation ) > > > > greetings, > > Florian > > -- > ------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) − 9131 − 85 26573 > Mailto: florian.haberl AT chemie.uni-erlangen.de > ------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
