Re: [gmx-users] Converting protonated protein with pdb2gmx

2010-10-29 Thread Deniz KARASU
Thanks Justin, I think that I have to write a script to remove hydrogens that are not suitable for united-atom forcefield. After this operation I can use pdb2gmx. On Fri, Oct 29, 2010 at 10:05 PM, Justin A. Lemkul wrote: > > > Deniz KARASU wrote: > >> Hi all, >> >> I'm trying to convert a prot

Re: [gmx-users] Converting protonated protein with pdb2gmx

2010-10-29 Thread Justin A. Lemkul
Deniz KARASU wrote: Hi all, I'm trying to convert a protein, that is protonated with another special software and by manually checking, with pdb2gmx. I am using FF53A6 forcefield and don't use -ignh option. When I run pdb2gmx it gives me this error. Atom HA in residue VAL 1 not found

[gmx-users] Converting protonated protein with pdb2gmx

2010-10-29 Thread Deniz KARASU
Hi all, I'm trying to convert a protein, that is protonated with another special software and by manually checking, with pdb2gmx. I am using FF53A6 forcefield and don't use -ignh option. When I run pdb2gmx it gives me this error. Atom HA in residue VAL 1 not found in rtp entry with 8 atoms