Hi Mark Sorry for the delayed reply. Somehow I missed your mail that time. I am doing exactly what you have suggested. I am building up this missing part and then trying to run the simulation. Again 'm sorry for this delay. Best regards, Abhik
Abhik Mukhopadhyay Departamento Química / Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa , 2829-516 Caparica, Portugal Mob. 00351912991251 http://xtal.dq.fct.unl.pt/ --- On Fri, 3/13/09, Mark Abraham <[email protected]> wrote: From: Mark Abraham <[email protected]> Subject: Re: [gmx-users] problem in energy minimization To: "Discussion list for GROMACS users" <[email protected]> Date: Friday, March 13, 2009, 7:55 PM Abhik Mukhopadhyay wrote: > Hi Jastin > My pdb2gmx command line is > pdb2gmx -ignh -f xx.pdb -o xxout.pdb -p xx.top -water spce > > When I created the topology it did not create a bond between those two residues (between which the part is missing). The above statement seems inconsistent with the observations below. > > I am trying to run a simulation on a xray structure that has 15 residues > missing. I have made the topology file accordingly. But after energy > minimization, the residues between which the portion is missing, got connected. > I tried an energy minimization with all-bonds constraint, but that i guess did > not do it properly. By far the most likely reason for the residues that should be spaced by the 15 missing residues to "get connected" was that your topology had an interaction defined. The fact that these residues were missing from the X-ray structure doesn't mean you should ignore their existence. Often they can be involved in useful chemistry. I would most likely consider using some (non-GROMACS) modelling software to "build in" such residues before attempting any MD. There are alternatives which involve capping the pseudo-termini and possibly using some kind of restraints, but these will be harder to defend to your paper's audience. Mark _______________________________________________ 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
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