Re: [gmx-users] problem in simulation of dna-protein complex
Hi Nitu, Check the atoms and their order in the pdb and the rtp file and try to find out which match and which miss. C2 amber99_2 0.56770 25 O amber99_41 -0.58810 26 I place my bet on this one. Cheers, Tsjerk -- 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 listgmx-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
Re: [gmx-users] problem during simulation of dna-protein complex
Hi Nitu, Energy minimization is only to remove some strain from your system. You probably don't want to include position restraints there. After energy minimization you typically run a short MD run in which you use position restraints such that the protein/DNA doesn't move to much, but the water can equilibrrate with respect to the protein. Check the tutorial material linked on the wiki. This stuff is mentioned in all of them. Cheers, Tsjerk On Wed, Jul 1, 2009 at 2:06 PM, nitu sharmasharmanit...@gmail.com wrote: Dear Tsjerk Thanks for your right suggestion. It works successfully for dna-protein complex simulation. i want to ask one more thing , can I use parameter file for energy minimisation which i have used for membrane protein simulation or can u suggest me what changes I have to make in parameter file to use for dna- protein complex simulation. the parameter file like this- cpp = /usr/bin/cpp define = -DPOSRE_PROTEIN constraints = none integrator = steep dt = 0.002 nsteps = 1 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.0001 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Specially where i have apply position restrain? Thanking you Nitu sharma ___ gmx-users mailing list gmx-us...@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 -- 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 listgmx-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
Re: [gmx-users] problem in simulation of dna-protein complex
nitu sharma wrote: Dear all , I am doing simulation of DNA-protein complex. Is anybody have idea about .hdb of DNA becoz in mannual nothing is wrritten about DNA hydrogen database .I have edited The database like this- ADE 9 2 6 H5* C5* C4* O5* 1 5 H4* C4* O4* C5* C3* 1 5 H3* C3* C2* C4* O3* 1 5 H2* C2* C3* C1* O2` 1 2 H2` O2` C2* C3* 1 5 H1* C1* N9 O4* C2* 1 1 H2 C2 N1 N3 2 3 H6 N6 C6 C5 1 1 H8 C8 N9 N7 But when I run pdb2gmx command on DNA-protein pdb file the error comes like this- Program pdb2gmx, VERSION 4.0.3 Source code file: h_db.c, line: 96 Fatal error: Error in hdb file ffoplsaano.hdb: Wrong number of control atoms (3 iso 4) on line: 1 5 H4* C4* O4* C5* If anybody have Idea what short of changes it needed please help me. The hydrogen database format is described in chapter 5. The description is not a work of art, but you should start looking there. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in simulation of DNA-protein complex
nitu sharma wrote: Dear all I am getting problem in running pdb2gmx command on DNA_protein file . The prblem is Program pdb2gmx, VERSION 4.0.3 Source code file: resall.c, line: 426 Fatal error: Residue 'T' not found in residue topology database So , actually I am unable to understand what should I do to solve this . Is it possible to get DNA.itp file from anywhere .If anyone have Idea about this please help me. Yes. Search the wiki for this error. Read chapter 5 of the manual. Describe your problem more fully. You haven't even told us your command line or forcefield :-) Read the page linked at the bottom of http://wiki.gromacs.org/index.php/Support Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem in simulation of DNA-protein complex
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_ residue_topology_database Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma Sent: Wednesday, 13 May 2009 5:25 PM To: gmx-users@gromacs.org Subject: [gmx-users] problem in simulation of DNA-protein complex Dear all I am getting problem in running pdb2gmx command on DNA_protein file . The prblem is Program pdb2gmx, VERSION 4.0.3 Source code file: resall.c, line: 426 Fatal error: Residue 'T' not found in residue topology database So , actually I am unable to understand what should I do to solve this . Is it possible to get DNA.itp file from anywhere .If anyone have Idea about this please help me. I really will be very thankful for him/her. Nitu sharma ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
