Re: [gmx-users] About pdb2gmx for cyclic pepetide

2012-09-14 Thread Mark Abraham
On 15/09/2012 1:37 PM, vidhya sankar wrote: Dear Justin and other Gromacs users , Thank you for your previous reply Again i Have tried the option -missing when i use pdb2gmx tool i have got errror as follows My command is ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p

[gmx-users] About pdb2gmx for cyclic pepetide

2012-09-14 Thread vidhya sankar
Dear Justin  and other Gromacs users ,     Thank you for your previous reply    Again i Have tried  the option -missing when i use pdb2gmx tool i have got errror as follows My command is ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p 2KDQ.top  -missing -ignh -ter There is a da

Re: [gmx-users] About pdb2gmx

2012-07-29 Thread Mark Abraham
On 30/07/2012 8:49 AM, Justin Lemkul wrote: On 7/29/12 9:39 AM, vidhya sankar wrote: Dear Justin Thank you for your previous reply When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum It runs successfully. But i have on issue. My PDB contains HIS residues in both chai

Re: [gmx-users] About pdb2gmx

2012-07-29 Thread Justin Lemkul
On 7/29/12 9:39 AM, vidhya sankar wrote: Dear Justin Thank you for your previous reply When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum It runs successfully. But i have on issue. My PDB contains HIS residues in both chain A and B I have selected GROMOS96 53a6 force

Re: [gmx-users] About pdb2gmx

2012-07-29 Thread tarak karmakar
see its not a big issue. Look at the atom types of the particular RESIDUE in the pdb file and also have a look into the atom types present in the rtp file. Now if these are matching properly then you can choose any convenient name for that particular residue in the rtp file. But the name of the par

[gmx-users] About pdb2gmx

2012-07-29 Thread vidhya sankar
Dear Justin Thank you for your previous reply When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro  -p 1OG2O.top   -renum It runs successfully. But i have on issue. My PDB contains  HIS residues in both chain A and B I have selected  GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) The .rtp f