[gmx-users] how to stop duplicate atoms from being deleted

Jennifer Williams Jennifer.Williams at ed.ac.uk
Mon Oct 26 13:35:44 CET 2009

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.

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   
>> 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
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School of Engineering
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