[gmx-users] how to stop duplicate atoms from being deleted
Jennifer.Williams at ed.ac.uk
Mon Oct 26 13:35:44 CET 2009
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.
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?
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 :) )?
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 alternative.
> 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
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