Re: AMBER: rdparm/ptraj writeparm + leap problem

From: David A. Case <>
Date: Wed, 17 Mar 2004 08:33:34 -0800

On Wed, Mar 17, 2004, wrote:

> I've managed to get it working most simply by just going back to the
> original file that I used to build the solvated system, and removing
> the ligand from there before writing a new prmtop file.

This is _usually_ done by editing the pdb file, (since that is thought to be
easier) although pulling the whole thing into leap and then removing atoms
should also work.

> To do this I had to delete first the atoms of the ligand (residue SG)
> remove complex complex.SG.34
> .....
> remove complex complex.SG.108
> then the residue itself
> remove complex complex.SG
> Leap (both xleap and tleap) were seg faulting if I attempted just one of the
> above two steps.

This sounds like the problem addressed in bugfix.46; have you applied that


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Received on Wed Mar 17 2004 - 16:53:00 PST
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