AMBER Archive (2009)

Subject: Re: [AMBER] xleap problem

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun Jan 25 2009 - 17:30:47 CST

On Sun, Jan 25, 2009, oguz gurbulak wrote:
>
> I tried to do a tutorial and a run a minimization in TUTOR?AL A2 as you
> said in order to control the min. process. And I didn't see anything wrong
> in TUTOR?AL A2 min.out file . I got the same min.out file in TUTOR?AL A2 .
> Before I start to use xleap for my n-dodecane simulation I did the
> operations below. After all these operations I started the min. , but I
> couldn't get the min.out file.

> sander -O -i min.in -o min.out -p n-dodecane.prmtop -c n-dodecane.inpcrd -r
> n-dodecane.rst

Well, *something* is different from what you are doing here than what
you did in the tutorial. But it is very unlikely that anyone on the
list will know what that is...you will need to carefully debug this
yourself. You need to experiment! Try things like

a. typing just "sander" with no arguments, or "sander --help". Do you
get obvious error messages?

b. with the full command above, does the command prompt immediately
return?

c. Leave out the "-O" option and see what happens.

d. try "sander -i min.in"

etc.etc.

As I said earlier, the problem probably has nothing to do with how you
set up the dodecane system -- at least, there is nothing you have
reported so far that would implicate the prmtop or inpcrd files as the
culpits.

...dac

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