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

[Justin A. Lemkul]

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" <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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 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

========================================