AMBER Archive (2003)

Subject: Re: saveAmberParm problems in xleap

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Tue May 06 2003 - 12:04:19 CDT

David Case wrote:

> The problem with both your mail and the one you cite is that no useful
> information is given to help find the problem. Saying "I ran leap on a
> protein and it crashed..." doesn't help much...you need to provide more
> specific information.

OK, I was using Amber7. I have a subsequence of
a protein about 70 amino acids (very standard,
no surprises). Basically, something like IL-8,
but it is a structure I am trying to figure out.
I used leaprc.ff99 in the start up.

It was originally a protein that I built using the
InsightII program. I want to feed the MD simulation
results I did with InsightII into Amber7. Naturally,
Accelrys & co introduced their idiosyncrasies
into the pdb files, so it took me a while before
I found a way to get LEaP to stop complaining.
I had to add two Cl- to the balance the charge of
the protein, and I wanted at least a 50x50x50 A^3
box to do the simulation in (preferably larger since
I have to do long simulations on the structure and
I want to minimize PBC effects as much as possible).

Using saveAmberParm in xleap, the top file came out ok,
but the crd file was empty. There were no error messages,
xleap simply died. I don't have it right here, but I
think it was a segmentation error, which can mean a lot
of things, but anyway, my first guess was memory.

It is on an IBM RS6000 with some 2Gb of memory. I had
to add the patches indicated on the Amber web page
before it would compile and install properly. The
tests ran ok, some differences, but nothing too bad.
I was able to get the small systems given in the
tutorial to work ok.

Whether any of these points are the problem or not, I
don't know, but that is the most description I can give
you short of send the pdb file. One clear annoyance
is the InsightII garbled-up pdb file. They won't let
you get out of anything without a fight.

hope that helps,
Wayne