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

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 23 20:11:18 CEST 2009

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 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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