Re: [gmx-users] in vacuo minimization of a multimeric protein
Dear Justin, thank you very much for suggestion. Now it works! Anna Message: 4 Date: Thu, 21 May 2009 10:39:33 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] in vacuo minimization of a multimeric protein To: Discussion list for GROMACS users Message-ID: <4a1567a5.5070...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > I'm trying to do a mild minimization on a homohexameric protein in vacuo. I > used the following options in the > em.mdp file: > > title = mild-mini > cpp = /usr/bin/cpp > define = -DFLEXIBLE > constraints = none > integrator = steep > nsteps = 500 > emtol = 5000 > emstep = 0.1 > nstcomm = 1 > ns_type = grid > nstlist = 5 > rlist = 0.9 > coulombtype = PME > rcoulomb= 0.9 > rvdw= 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft= yes > > I simply converted my protein from .pdb format to .gro using pdb2gmx, and > then I submitted immediately to > minimization, since I only would like to relieve some eventual steric clashes > between subunits, without > proceed with a further MD simulation and without distorting too much the > protein structure. > At the end of the run I found that the 6 subunits of my protein (which are > not covalently linked to each > others) are separated in two dimers and two monomers. I tried also the > minimization in water, although for > this system I don't want water, but the result is not changing: the protein > separates in subunits. The same if > I apply PBC (the first time I applied it, then I saw that the subunits > separated, I check the gmx-users list > and delete pbc from the em.mdp, but the results are quite the same). I also > changed ns_type to simple, without > success. Have you got any suggestion? Thanks in advance If you have gone straight from pdb2gmx to grompp, then your box size is likely inappropriate. Use editconf -c -d to define a suitably large box. -Justin > Anna > __ > Anna Marabotti, Ph.D. > Laboratory of Bioinformatics and Computational Biology > Institute of Food Science, CNR > Via Roma 64 > 83100 Avellino (Italy) > Phone: +39 0825 299651 > Fax: +39 0825 781585 > Skype: annam1972 > E-mail: amarabo...@isa.cnr.it > Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm > > "If you think you are too small to make a difference, try sleeping with a > mosquito" > > ___ ___ 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] in vacuo minimization of a multimeric protein
Anna Marabotti wrote: Dear gmx-users, I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in the em.mdp file: title = mild-mini cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 emtol = 5000 emstep = 0.1 nstcomm = 1 ns_type = grid nstlist = 5 rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes I simply converted my protein from .pdb format to .gro using pdb2gmx, and then I submitted immediately to minimization, since I only would like to relieve some eventual steric clashes between subunits, without proceed with a further MD simulation and without distorting too much the protein structure. At the end of the run I found that the 6 subunits of my protein (which are not covalently linked to each others) are separated in two dimers and two monomers. I tried also the minimization in water, although for this system I don't want water, but the result is not changing: the protein separates in subunits. The same if I apply PBC (the first time I applied it, then I saw that the subunits separated, I check the gmx-users list and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple, without success. Have you got any suggestion? Thanks in advance If you have gone straight from pdb2gmx to grompp, then your box size is likely inappropriate. Use editconf -c -d to define a suitably large box. -Justin Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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
[gmx-users] in vacuo minimization of a multimeric protein
Dear gmx-users, I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in the em.mdp file: title = mild-mini cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 emtol = 5000 emstep = 0.1 nstcomm = 1 ns_type = grid nstlist = 5 rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes I simply converted my protein from .pdb format to .gro using pdb2gmx, and then I submitted immediately to minimization, since I only would like to relieve some eventual steric clashes between subunits, without proceed with a further MD simulation and without distorting too much the protein structure. At the end of the run I found that the 6 subunits of my protein (which are not covalently linked to each others) are separated in two dimers and two monomers. I tried also the minimization in water, although for this system I don't want water, but the result is not changing: the protein separates in subunits. The same if I apply PBC (the first time I applied it, then I saw that the subunits separated, I check the gmx-users list and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple, without success. Have you got any suggestion? Thanks in advance Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" ___ 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
