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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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