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" <[email protected]> Subject: Re: [gmx-users] in vacuo minimization of a multimeric protein To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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: [email protected] > 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 list [email protected] 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
