AMBER: RE: antechamber

From: Ross Walker <>
Date: Tue, 9 Oct 2007 09:51:57 -0700

Hi Fatima

I am copying this to the amber mailing list (see
for signup details) since this is the best place for such messages as then
both the questions and replies get archived at and can be searched by others.

> my molecular structure contains two groups of SO3Na when i
> tried Antechamber
> to get prepin file it did not recognise the Na type as a
> sodium but because it
> is defined as another type for Nitrogen. So to work around
> this, i removed Na+
> which left me with the so3- group and this time antechamber
> worked and i got
> my molecule loaded into Leap. Then i used one of the utilites
> to neutralise it
> by adding Na+.
> At this stage i wonder if there is a way to place Na+ nearby
> the original
> location of the bonded Na

The key is that while sodium ions have atom type Na there actual name in the
template library for a sodium residue is Na+. Hence in a pdb file to be read
by leap it would be residue name Na+ and atom name Na+. You could also try
this again with Antechamber and see if it recognized it properly then.

Another option is to go back to leap and load the prep file created by
antechamber for so3- but then load the original pdb file you have with the
sodium atoms in there, making sure they are in seperate residues to the so3-
and named Na+ in both the atom name and residue name column (make sure you
keep the spacing correct).

An alternative is to edit your inpcrd file to manually change the
coordinates of the sodium ion but this could be quite time consuming.

Another option would be to do targetted MD. essentially add a restraint to
the sodium atom that pulls it towards the so3- group. Then when they get
close you can turn off the restraints.

The first option of loading the original pdb into leap will likely be the

Good luck.

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Oct 10 2007 - 06:07:50 PDT
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