Re: AMBER: Lone pairs in antechamber

From: David A. Case <>
Date: Thu, 30 Oct 2008 10:27:31 -0400

On Thu, Oct 30, 2008, Diddo Diddens wrote:
> I would like to continue a simulation of an equilibrated structure (100 DME
> molecules) which was generated by another MD program. This program uses extra
> points as lone pairs located at the oxygen atoms (0.5 Angstroems apart). I
> write out the atom positions of the structure to a pdb file.

If you want to continue the simulation generated by another MD program, you
would have to implement whatever force field that other program used into

Amber has some lone-pair capabilities, which may or may not be equivalent to
what the other program used or assumed. Since documentation is sparse, you
would have to study the code to see how lone pairs work here. Since you say
you are new to Amber, this is unlikely to be an easy or simple task.

Antechamber is the program to apply the general Amber force field (GAFF) to
molecules. GAFF does not use lone pairs, so antehcamber won't be of much
help. Unless: if you want to continue the simulation using GAFF (without lone
pairs), then strip the lonepair records from the input PDB file, then

...good luck...dac

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Received on Fri Oct 31 2008 - 05:10:43 PDT
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