Re: [gmx-users] How to make a pdb file for methane pair?

Hi, Justin: I put a residue name ( ALA) there, but pdb2gmx told me that there is a fatal error: Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation stat

Re: [gmx-users] How to make a pdb file for methane pair?

xianghong qi wrote: Hi, Justin: I put a residue name ( ALA) there, but pdb2gmx told me that there is a fatal error: Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a

Re: [gmx-users] How to make a pdb file for methane pair?

Thanks so much , Justin. I will try. -Xianghong Qi On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > xianghong qi wrote: > >> Thanks, so how to edit a residue name ? I am confused. sorry about such >> simple question. >> > > Use a text editor. Be sure to keep t

Re: [gmx-users] How to make a pdb file for methane pair?

xianghong qi wrote: Thanks, so how to edit a residue name ? I am confused. sorry about such simple question. Use a text editor. Be sure to keep the formatting right when doing so: http://www.wwpdb.org/documentation/format32/sect9.html -Justin -Xianghong Qi On Tue, Oct 21, 2008 at 9:0

Re: [gmx-users] How to make a pdb file for methane pair?

Thanks, so how to edit a residue name ? I am confused. sorry about such simple question. -Xianghong Qi On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <[EMAIL PROTECTED]>wrote: > xianghong qi wrote: > >> Hello, everyone, >> I want to create a pdb file for methane pair . I can make methane pair >>

Re: [gmx-users] How to make a pdb file for methane pair?

xianghong qi wrote: Hello, everyone, I want to create a pdb file for methane pair . I can make methane pair from MOE and then save to pdb file format without any residue name there. The question is that I can't convert pdb file to .gro file from gromacs without residue name. Anyone has any ide

[gmx-users] How to make a pdb file for methane pair?

Hello, everyone, I want to create a pdb file for methane pair . I can make methane pair from MOE and then save to pdb file format without any residue name there. The question is that I can't convert pdb file to .gro file from gromacs without residue name. Anyone has any idea about this question. I