[gmx-users] How to make a pdb file for methane pair?
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 22 17:58:48 CEST 2008
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 different protonation state.
> Option -ignh will ignore all hydrogens in the input.
Right, if it's not alanine, then that won't work.
> If I creat one ( CH4), it said that :
> Residue 'CH4' not found in residue topology database.
>
Pretty common error; see here:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
If the residue/molecule name is not already parameterized and entered into the
.rtp file, you'll have to come up with the topology yourself. For methane, this
should be quite easy to do by hand.
-Justin
> my pdb file for methane pair is ( I created from MOE), original residue
> name is *, now I change to CH4:
> REMARK 99 MOE v2007.09 (Chemical Computing Group Inc) Mon Oct 20
> 12:31:39 2008
> HETATM 1 C CH4 1 -0.415 -0.007 0.005 0.00
> 0.00 C
> HETATM 2 H2 CH4 1 -0.778 0.720 0.731 0.00
> 0.00 H
> HETATM 3 H3 CH4 1 -0.778 -0.999 0.271 0.00
> 0.00 H
> HETATM 4 H4 CH4 1 -0.778 0.259 -0.988 0.00
> 0.00 H
> HETATM 5 H1 CH4 1 0.675 -0.007 0.005 0.00
> 0.00 H
> HETATM 6 C CH4 2 9.588 -0.007 0.005 0.00
> 0.00 C
> HETATM 7 H1 CH4 2 10.678 -0.007 0.005 0.00
> 0.00 H
> HETATM 8 H2 CH4 2 9.225 0.720 0.731 0.00
> 0.00 H
> HETATM 9 H3 CH4 2 9.225 -0.999 0.271 0.00
> 0.00 H
> HETATM 10 H4 CH4 2 9.225 0.259 -0.988 0.00
> 0.00 H
> CONECT 1 2 3 4 5
> CONECT 6 7 8 9 10
> END
>
> What kind of residue name I should put there? thanks lot.
> -Xianghong Qi
>
>
> On Wed, Oct 22, 2008 at 9:56 AM, xianghong qi <xianghong001 at gmail.com
> <mailto:xianghong001 at gmail.com>> wrote:
>
> Thanks so much , Justin. I will try.
> -Xianghong Qi
>
>
> On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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 the formatting right when
> doing so:
>
> http://www.wwpdb.org/documentation/format32/sect9.html
>
> -Justin
>
> -Xianghong Qi
>
>
> On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>
> 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 idea
> about this
> question. I appreciate
> your help.
>
>
> You don't need a .gro file for itself.. see
>
> http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
>
> You'll need a residue name to get a topology defined, so
> edit one in.
>
> Mark
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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