Re: [gmx-users] md with multiple ligands

2013-02-14 Thread Justin Lemkul
-- Message: 8 Date: Wed, 13 Feb 2013 08:28:00 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] md with multiple ligands To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 511b94e0.4040...@vt.edu Content-Type: text

[gmx-users] md with multiple ligands

2013-02-13 Thread Ansuman Biswas
Dear gromacs users, I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force field. Its a dimeric protein with a MG ion and 2 ligands bound to two active sites. I wish to run the dimer and there would be 4 ligands. I generated the topology files (.itp) of ligands using SWISSPARAM.

Re: [gmx-users] md with multiple ligands

2013-02-13 Thread Justin Lemkul
On 2/13/13 5:24 AM, Ansuman Biswas wrote: Dear gromacs users, I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force field. Its a dimeric protein with a MG ion and 2 ligands bound to two active sites. I wish to run the dimer and there would be 4 ligands. I generated the

[gmx-users] md with multiple ligands

2013-02-13 Thread Ansuman Biswas
-- Message: 8 Date: Wed, 13 Feb 2013 08:28:00 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] md with multiple ligands To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 511b94e0.4040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed