[gmx-users] how to stop duplicate atoms from being deleted
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 26 15:14:14 CET 2009
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
> 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
> 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
> 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.
> Thanks -I am learning a lot from your advice
> Quoting "Justin A. Lemkul" <jalemkul at 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
>> 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
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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