[gmx-users] Re: NADP inferno

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Tue Apr 8 15:42:01 CEST 2003

Dear Sergio,

If you look at FAQ´s at the PRODRG web, you will find:

Q: Why does PRODRG insist on renaming my atoms? This is a major pain
when I'm sumitting my structure to the PDB!

     A: Most refinement programs require unique atom identifiers
(names). PRODRG therefore checks for duplicate atoms names in your
input, and if it finds them all
     atoms are renamed. You can prevent this by using a simple trick.
Consider ...

Maybe you can find some help there!

I´ve recently solved the same problem for a small ligand topology for
GROMOS96. I´ve used the GROMOS87 topology generated by PRODRG (I think
it works better if your input is a plain text picture) and converted to
GROMOS96 by hand comparing the parameters in the ifp file for G87 and
G96. Then you have to check wether all bond, angle, dihedral parameters
are OK. I saw some little problems with the chirality, some dihedrals,
angles... This is really tedious, but you can get it!
Hope this help!
with best wishes,

"Tanos C. C. França" wrote:

> Dear Sergio,
> I have faced recently this problem and I think I solved it simply by
> choosing the option "0" (gromacsforcefield) 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,
> after
> takingDaan's andDavids advices into account decided to generate the
> of it through PRODREG, then simulate it in vacuum, then in water and
> then
> with the protein.
> The first errror in this path is when using PDB2GMX (I use the PDB
> with
> polarhydrogens only) :
> Fatal error: Atom NBO in residue NADP 1 not found in rtp database
> while sorting atoms
> The atomic nomenclature from Prodreg is incorrect! ..usingGromos ore
> Gromacs force field
> Stuck!
> Sergio
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Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144,  28006  MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18

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