[gmx-users] Using specbond.dat in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Thu Jun 12 07:51:15 CEST 2014

On 6/11/14, 2:33 PM, Matthew Stancea wrote:
> ? Hello,
> I have been having a bit of issues generating an accurate gromacs topology
> file ("topol.top") utilizing a pdb of a cyclic peptide in pdb2gmx. I have
> been able to generate topologies that are almost identical to the original
> pdb using the option "-ignh" at the end of my command, but doing so deletes
> the bond between the first nitrogen and the last carbon (which should be
> connected for this peptide to be cyclic) and adds two additional hydrogens
> and a positive charge to the first nitrogen and an additional oxygen and a
> negative charge to the last carbon, rendering this peptide as non-cyclic.
> After searching around for quite a while, I found out that many others on
> this mailing list were having the same issues as myself, and some replies to
> their messages including the usage of a file known as "specbond.dat" which
> may be helpful in retaining that bond.

The -ignh flag is not relevant to those observations.  Construction of termini 
and assignment of ionization state is done with -ter.  For your case, you likely 
need to be using -ter and selecting "None."

> However, I could not find an explanation of how to use this file in my
> command, and I was hoping someone could guide me on how to use specbond.dat
> in order to specify a particular bond. (I have tried both "-chainsep
> specbond.dat" and "-merge specbond.dat".)

specbond.dat is a standard file that is always read by pdb2gmx; it is not an 
input option.  It lives in $GMXLIB but can be overridden by a copy in the local 
directory (as with all Gromacs library files).

> I have been able to make a specbond.dat file that thoroughly explains what
> special bonds I need pdb2gmx to account for, but when I have tried to type a
> command file to use it, pdb2gmx generates topology files nearly identical to
> the topologies of the non-cyclic peptides when I had used the "-ignh" option
> rather than generating a cyclic peptide topol.top.
> If more specific information is needed, I can provide that; however, I am not
> looking for an answer that is specific to my own issue, but rather a tutorial
> into generating a topology for gromacs from a pdb file of a cyclic peptide by
> using specbond.dat with pdb2gmx. (My version of pdb2gmx is 4.6.2.)

Post the contents of your version of specbond.dat, the exact command you're 
issuing, and any screen output related to parsing of specbond.dat.  You should 
only need to add one bond to the one that is provided by default.  Your version 
of specbond.dat is either in $GMXLIB or the working directory, correct?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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