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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Thanks so much , Justin. I will try.
-Xianghong Qi
On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[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 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
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>> 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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Some people make the world more special just by being in it.
--
Some people make the world more special just by being in it.
--
========================================
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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