[gmx-users] Re: NADP inferno

Tanos C. C. França tccf at epq.ime.eb.br
Tue Apr 8 13:44:01 CEST 2003

      Dear Sergio,
      I have faced recently this problem and I think I solved it simply
by choosing the option “0” (gromacs forcefield) when running pdb2gmx. I
am afraid this kind of problem happens because PRODRG runs with GROMOS
87 and do not recognize GROMOS 96.
      Best regards.
      Tanos C. C. Franca
      IME – Rio de Janeiro - Brasil 
Message: 4
Date: Mon, 07 Apr 2003 17:00:52 +0200
To: gmx-users at gromacs.org
From: Sergio Manzetti <sergio.manzetti at bio.uio.no>
Subject: [gmx-users] NADP inferno
Reply-To: gmx-users at gromacs.org
Hi all, in regard with NADP in simulation with this protein I have,
taking Daan's and Davids advices into account decided to generate the
of it through PRODREG, then simulate it in vacuum, then in water and
with the protein.
The first errror in this path is when using PDB2GMX (I use the PDB with 
polar hydrogens only) :
Fatal error: Atom NBO in residue NADP 1 not found in rtp database
              while sorting atoms
The atomic nomenclature from Prodreg is incorrect! ..using Gromos ore 
Gromacs force field

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