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

[xianghong qi]

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.
If I creat one ( CH4), it said that :
Residue 'CH4' not found in residue topology database.

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>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> 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>> 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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>
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> Some people make the world more special just by being in it.
>



-- 
Some people make the world more special just by being in it.
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