Jennifer Williams wrote:
Hi Justin,
Thanks for the new suggestion.
However, wouldn't this again involve the sorting of my .pdb file?
I have modified the specbond.dat
3
MSI SI 4 MO O 2 0.16 MCM MCM
MSI SI 4 MOH OH 2 0.16 MCM MCM
MOH OH 2 MH H 1 0.101 MCM MCM
BUT the specbond.dat is called after the duplicate atoms are deleted:
Now there are 4 atoms. Deleted 4280 duplicates.
Opening library file
/home/jwillia4/gromacs-4.0.5/code/share/gromacs/top/specbond.dat
3 out of 3 lines of specbond.dat converted succesfully
So at present my pdb file is shortened down to 4 atoms before specdat
even gets a chance to work on it.
You need separate residues, and if necessary, separate names for different
residue types.
The only solution I can see to this is to rename each and every atom in
my .pdb file with a different residue number and name. This then means
that I would need a huge specbond.dat where the bonds were defined for
each of these residues-this would essentially mean defining thousands of
bonds as I wouldn't be able to define the bonds by atom type but by
their individual reside number. Is this correct or am I missing something?
You don't need a huge specbond.dat; as I see it, you only have nine possible
types of residues - those around the edges, and interior ones. I will send you
a test case (off-list) that worked for me.
What I really would like is to stop the program deleting these duplicate
atoms-then I could use pdb2gmx to generate the entire topology file. Do
you know a way of doing this (and here I am really hoping that I don't
have to mess with the source code :) )?
Unfortunately, you cannot do this without modifying the source, and pdb2gmx is a
big program that is somewhat difficult to work with.
-Justin
Thanks -I am learning a lot from your advice
Jenny
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
Justin A. Lemkul wrote:
I can see how this rapidly becomes difficult :) I don't believe
that pdb2gmx can handle such "multi-directional" bonding, since the
residues that are connected are not necessarily numerically
sequential.
I should amend this statement (typing quicker than the brain can keep
up!) - It is not that pdb2gmx cannot handle multi-directional bonding,
it is moreso that I don't think it cannot be done using the +/-
convention of the .rtp files.
Using specbond.dat, as I suggested before, should be a viable
alternative.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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