On 10/6/12 1:57 PM, Elie M wrote:
Yes I just saw that. thanks for turning my attention. The top file assigned
this order of the atoms....do you think switching the order of the atoms in the
top file would solve the problem?
In principle, I don't think it should matter, but it's something you can check
yourself in less time than it takes to send an email :)
-Justin
Elie
Date: Sat, 6 Oct 2012 13:26:38 -0400
From: [email protected]
To: [email protected]
Subject: Re: [gmx-users] Error with "grompp"
On 10/6/12 1:18 PM, Elie M wrote:
This is what I did. For example one of the [bonds] problems is a bond between S and one
of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S
because it si related to " all-atom S: thiophenol (HS is #204)"; the
corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two:
the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a
line:
SH CA 1 0.15925 186649.5 ;
However the error related to this bond is still present. I was just thinking
mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol
is SH?? maybe this is the source of the error and I have to redefine things in
the .n2t file?
It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell
by the mass in atomtypes.atp and the fact that the first letter is S). The
corresponding H atom is HS, so that's not the problem. The parameters for this
bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5
version):
CA SH 1 0.17400 209200.0 ; wlj
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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