[gmx-users] pdb2gmx -water

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 18 22:05:34 CEST 2009

Paymon Pirzadeh wrote:
> Hello,
> I am trying to use a different water model for my proteins (using oplsaa
> force field). I use the .itp file which I developed, but pdb2gmx does
> not accept it. I am a bit confused on how I can make my water model work
> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
> need to change the names of my particles in my water .itp file by
> including _FF_OPLS?

I don't know how pdb2gmx decides how to recognize water models; it may be 
hard-coded.  In any case, your atom types have to be consistent with OPLS 
standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file, 
you may not need it if OPLS is the only force field with which it will be used. 
  The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.


> Regards,
> Payman 
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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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