[AMBER] Free energy perturbation of Ca2+ ion

From: Sergey Samsonov <sergeys.biotec.tu-dresden.de>
Date: Fri, 10 Jun 2011 15:50:37 +0200

Dear AMBERs,

I'm trying to apply FEP double decoupling method for Ca2+ annihilation
in explicit solvent. For this I use Ca2+ residue library (using Ca2+
Aqvist JPC 1990,94,802. adapted). I use 2 topology files and run
multisander with the group file as it is described in the tutorial A6.
For electrostatic component everything works without any problem, the
topology files in this case differ only in the charge value. For VDW
component perturbation I use zero charges for both topologies and DC
(Dummy calcium) in one of the files. The parameters I load for C0 (Ca2+)
and DC (Dummy calcium) look simply like this:

C0 1.7131 0.459789 Ca2+ Aqvist JPC
DC 0.0000 0.0000 Dummy Ca2+
C0 40.08 calcium
DC 40.08 Dummy calcium

However, when I save the parameters for the atom with DC atomic type, I
get the following error:

> > saveamberparm x dummy.top dummy.crd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<Ca2 1>.A<Ca 1> Could not find type: DC
Parameter file was not saved.

At the same time the command "check x" does not find any problems with
the unit. I also tried to create a library of dummy Ca first but the
error is the same.
The last time I used FEP, I still used one perturbed prmtop file in
AMBER 8, then the same kind of dummy atoms description worked, so it
does not look like lack of parameters.

What could be the sorce of the problem?

Thank you very much in advance and best regards,


Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax:   (+49) 351 463 402 87 
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
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Received on Fri Jun 10 2011 - 07:00:03 PDT
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