AMBER Archive (2004)

Subject: Re: AMBER: rdparm/ptraj writeparm + leap problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 17 2004 - 10:33:34 CST

On Wed, Mar 17, 2004, david.evans_at_ulsop.ac.uk wrote:

> I've managed to get it working most simply by just going back to the
> original leap.in 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
patch?

...dac

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