AMBER Archive (2009)

Subject: Re: [AMBER] xleap problem

From: David A. Case (
Date: Sun Jan 25 2009 - 07:57:41 CST

On Sun, Jan 25, 2009, oguz gurbulak wrote:

> I?m trying to get the prmtop and inpcrd files for my n-alkanes
> simulations with using xleap. My leap.log file is in below. I want to
> do MD simulations for 100 n-dodecane  molecules. I attached the related
> files to the mail. I used packmol in order to get my pdb file that
> includes 100 n-dodecane  molecules. Then I started the minimization, but
> the min. progress stopped and I got an empty min.out file. I thought
> that I couldn?t get the prmtop and inpcrd files  succesfully. Could you
> please help me to solve this problem and get prmtop and inpcrd files
> succesfully with xleap ?

If you try to run sander and get an empty min.out file, that probably
has nothing to do with whether you are running dodecane or something
else, or with the nature of your prmtop and inpcrd files.

Run a simple sander minimization from the tutorials, so that you have a
working example. Then change substitute your prmtop and inpcrd file and
run again. Try to localize the differences between what works and what

I don't think anyone on the list can help much right now: your problem is
with the minmization step, but the only information you provided in your
email was about the LEaP part. That is: you provided lots of information
about the things that (apparently) worked fine, but no information about
the step that failed.


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