Re: [AMBER] Problem with GDP parameters generation

From: FyD <>
Date: Sun, 11 Dec 2011 20:09:42 +0100

Dear Neeru,

With Antechamber, I would first check if chemical equivalencing is
correctly applied; i.e. the charge values for chemical equivalent
atoms should be equivalenced (if you use the RESP program, this is
usually done during the charge fitting step). From the last examples I
saw it seems that chemical equivalencing is not handled by
Antechamber; this looks quite weired to me... If this is indeed
confirmed (check that carefully) my personal opinion is that this is
bad. Ante_R.E.D._2.0 . R.E.D. Server has been designed to correctly
handle chemical equivalencing for atoms and groups of atoms.

Another common problem with GMP, GDP, GTP etc... is that the entire
molecule is negatively charged and consequently the optimized geometry
obtained after geometry optimization and involved in charge derivation
is unlikely to be representative of the experimental conditions. An
alternative is to use the building block approach were the
conformation(s) of the different elementary constituents of GMP, GDP
and GTP involved in charge derivation are rigorously defined. R.E.D.
IV at R.E.D. Server does handle this building block approach and
potentially can generate any type of molecular fragment starting from
a whole molecule or a set of whole molecules.

Finally, we are developing a new feature in R.E.D. IV (it should be
available soon) where the molecular fragments are directly connected
by the R.E.D. program. Indeed, the LEaP program (i.e. t/xLEaP) is very
powerful, but has limitations (bugs) when one wishes to connect any
type of molecular fragments together.

So I would like to suggest you to use our tools .; besides, the R.E.D. tools, a server
and a database you will find there many tutorials...

regards, Francois

> I have to simulate a protein-GDP complex. For this,I have generated Amber
> topology and coordinate files for GDP molecule after preparing GDP.lib and
> frcmod.GDP.
> But the topology and co-ordinates file are quite different from the input
> PDB file and hence the parameters are also faulty, the GDP molecule is not
> fitting in the binding pocket of protein (Upon superimposition of the
> generated topology and coordinate file with the initial PDB input file,
> they were not being superimposed).
> Upon tracking the whole process, it was found that the error might be while
> using antechamber for generating prepin file using Gaussian output file as
> the input.
> Can anyone please suggest some way to apply some constraints in the
> antechamber command itself. OR if anybody has the paramters or topology for
> GDP, can anyone provide me the same so that I can compare and see where the
> parameters are differing.

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Received on Sun Dec 11 2011 - 11:30:02 PST
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