AMBER Archive (2003)

Subject: Re: problem with "Example 3" tutorials

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Wed Mar 26 2003 - 11:35:11 CST

Hi
i think the error could be because of -c option that u have used. You
should be giving the coordinate file that is generated using leap

command should be like

sander -O -i gcg.in -p prmtop.gcg -c prmcrd.gcg -r restart.x -o gcg.out

where
prmcrd.gcg is coordinate file generated using leap
and -r restart.x is the restart file generated by sander (all coordinate
info is stored here.

Regards
-Venkat

On Tue, 25 Mar 2003, S.Swaminathan wrote:

>
> hi
>
> I am working on AMBER tutorials. I am facing a problem in Example 3 when I
> am trying to run sander by invoking (on Page 29 in the AMBER manual) :
>
>
> sander -O -i gcg.in -p prmtop.gcg -c gcg_start.x -o gcg.out
>
> (here gcg.in contains "Minimize water and ions" script.
> prmtop.gcg is obtained from Running tleap.)
>
>
> I am getting the following error from the above program:
>
> ==========================================================================
> Unit 10 Error on OPEN: refc can't close stderr: [1001] illegal unit number
> logical unit 0, named 'stderr'
> Abort (core dumped)
>
> ==========================================================================
>
> how do i rectify this ? what is the reason for this ?
>
> thanks
> Swaminathan
>
>
>
>
>
>
>
>
>
>
>
>
>
> ======================================================
> S.Swaminathan
> Technical Officer - Bioinformatics
> Centre for DNA Fingerprinting & Diagnostics (CDFD)
> ECIL Road, Nacharam,
> Hyderabad - 500 076
> Tel: 27151344,346 Extn. 1207/1208
> ======================================================
>
>