[gmx-users] Using specbond.dat in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 23:16:46 CEST 2014

On 6/18/14, 5:08 PM, Matthew Stancea wrote:
>>>>> After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon.
>>>> You need to be using -ter and choosing "None" for both termini, otherwise the
>   default behavior takes over and pdb2gmx builds ionized termini.  You don't have
>   free termini, so you have to take control of pdb2gmx.
>>> I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter
>   " and was asked about the protonation states for two of the residues, but I was not asked about the termini.
>> Ah, because it's Amber.  Amber force fields are special and have specific
> nomenclature that signifies N- and C-termini, so they automatically get built.
> Changing the residue names by removing the N and C prefixes should fix things.
> Okay, which file do I remove the N and C prefixes from?

Coordinate file, always manipulate the coordinate file.

But the fact that you're asking this tells me that likely you never actually 
added those prefixes, so pdb2gmx is being "smart" and adding them for you.  In 
that case, there's nothing you can do short of (1) modifying the pdb2gmx code, 
(2) manually hacking the topology - ugly, but effective, or (3) using a 
different force field that doesn't have terminus-specific naming (anything 
that's not Amber).



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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