Re: [gmx-users] Error in ligand coordinate file

On 8/9/12 6:31 AM, sai nitin wrote: Hi justin, Yes swiss param gave me ligand.itp file which gromacs topologies i included in topol.top file which i generated ..usign PDB2GMX so no need of creating seperate topol.top file for ligand only? can i use same topol.top file to run MD to simulate onl

Re: [gmx-users] Error in ligand coordinate file

Hi justin, Yes swiss param gave me ligand.itp file which gromacs topologies i included in topol.top file which i generated ..usign PDB2GMX so no need of creating seperate topol.top file for ligand only? can i use same topol.top file to run MD to simulate only ligand because current topol.top file

Re: [gmx-users] Error in ligand coordinate file

On 8/8/12 10:44 AM, sai nitin wrote: Hi justin, Ok i will explain more clearly what i really have is protein ligand complex from Autodock..I choose best complex based on predicted binding affinity. Using pymol i visualized complex.pdb and saved only ligand (ligand.pdb given below) and used sw

Re: [gmx-users] Error in ligand coordinate file

Hi justin, Ok i will explain more clearly what i really have is protein ligand complex from Autodock..I choose best complex based on predicted binding affinity. Using pymol i visualized complex.pdb and saved only ligand (ligand.pdb given below) and used swiss param tool online http://swissparam.c

Re: [gmx-users] Error in ligand coordinate file

On 8/8/12 5:37 AM, sai nitin wrote: Hi justin, Thanks for reply now i have ligand corrdinate file as follows ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C ATOM 3 C A -13.037

Re: [gmx-users] Error in ligand coordinate file

Hi justin, Thanks for reply now i have ligand corrdinate file as follows ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C ATOM 3 C A -13.037 -14.131 1.869 -0.32 -0.03 C

Re: [gmx-users] Error in ligand coordinate file

On 8/7/12 5:08 AM, sai nitin wrote: Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Char

[gmx-users] Error in ligand coordinate file

Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Charmm 27 FF second one is simulate ligand i