[gmx-users] simulation of protein in presence of ATP

Lucio Ricardo Montero Valenzuela lucioric at ibt.unam.mx
Mon Jun 22 09:55:12 CEST 2009

Hi nikhil damle
When running pdb2bmx for ATP in a PDB file using the ffG43a1, shows
warnings because atom names don't match. You have to cut the ATP
coordinates out to other PDB file, to convert it to gromacs format
(.gro) using editconf and edit this file in gromacs format to match the
atom namings in the rtp file. Then, one can run pdb2gmx to that file in
gromacs format to generate the topology for the ATP. When you have
gotten this topology file, you can change its extension to ITP. By other
side you need to run pdb2gmx for the rest of the molecule. Then you can
merge the .gro files and the topology files, as explained in the GROMACS
Tutorial for Drug-Enzyme Complex
PhD. Student
Lab. Dr. Federico Sanchez
Instituto de Biotecnologia, UNAM

El lun, 22-06-2009 a las 10:09 +0530, nikhil damle escribió:
> Hi all,
>        I want to carry out a MD simulation of a receptor protein in
> presence of ATP molecule. ATP is included in .rtp file of ffG43a1
> force field. but  post pdb2gmx, .pdb output file does not show crds of
> ATP. Does it mean that ATP is not recognized as a residue of protein
> in spite of being included in .rtp file. If so how does one carry out
> this simulation ? If .itp file of ATP is an option, how can one get
> the specific values of charges etc for constructing .itp file. Manual
> does not mention anything regarding it. 
>       Please help as soon as possible.
> Regards,
> Nikhil
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