Re: [gmx-users] Issue in Energy minimization protein-ligand complex

2013-07-04 Thread Justin Lemkul
On 7/4/13 3:16 PM, Sainitin Donakonda wrote: Hi Justin, Thanks for reply. using pdbgmx i generated charmm27 force field for protein I prepared ligand topologies using swissparam online tool for all 5 ligands. But it worked for 4 and 5th one is creating problem at energy minimization step.

Re: [gmx-users] Issue in Energy minimization protein-ligand complex

2013-07-04 Thread Sainitin Donakonda
Hi Justin, Thanks for reply. using pdbgmx i generated charmm27 force field for protein I prepared ligand topologies using swissparam online tool for all 5 ligands. But it worked for 4 and 5th one is creating problem at energy minimization step. Thanks -sainitin On Thu, Jul 4, 2013 at 9:02 PM,

Re: [gmx-users] Issue in Energy minimization protein-ligand complex

2013-07-04 Thread Justin Lemkul
On 7/4/13 3:00 PM, Sainitin Donakonda wrote: Hi all, I have set of 5 different drugs which are complexed with same protein (homology model). So i wanted to run MD simulation using gromacs. I followed one procedure as follows 1) I took homology model and minimized it 2) Then followed general p

[gmx-users] Issue in Energy minimization protein-ligand complex

2013-07-04 Thread Sainitin Donakonda
Hi all, I have set of 5 different drugs which are complexed with same protein (homology model). So i wanted to run MD simulation using gromacs. I followed one procedure as follows 1) I took homology model and minimized it 2) Then followed general procedure of simulation in gromacs. 4 drugs with