AMBER Archive (2008)

Subject: Re: AMBER: problem in starting sander

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Sun Jun 08 2008 - 21:40:52 CDT

Dear Ross,

I have one 6lyzwatmin1.out file, however, nothing in it, no start up
information, no error message. I am sure my prmtop file has ions and
solvent. Does that mean my molecule is in solvent environment?

Qiuting Hong

On Sun, Jun 8, 2008 at 3:30 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Qiuting
>
>
>
> What exactly do you mean by " I can't see any output result in *6lyzwatmin1.out
> *even the job run for a long time"?
>
> Do you not get any output file at all? Or the output file exists, contains
> some info but only effectively start up information? If so then what is the
> last line in the output file?
>
>
>
> Normally you can get this problem when you have a gas phase or implicit
> solvent prmtop and inpcrd file but set ntb=1. Sander then hangs trying to
> read the box info from the inpcrd file when that info doesn't exist. So
> check your prmtop and inpcrd file contain box information and are setup for
> a periodic system.
>
>
>
> Failing that please clarify what exactly the problem is. Also do all the
> test cases run fine?
>
>
>
> All the best
>
> Ross
>
>
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Qiuting Hong
> *Sent:* Sunday, June 08, 2008 11:26 AM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: problem in starting sander
>
>
>
> Dear all,
>
>
>
> I am trying to run MD for lysozme in explicit water. However, I have a
> problem in starting sander. I never has a problem like this before.
>
> Below is what I did:
>
>
>
> *[258] castalia.sfsu.edu>$AMBERHOME/exe/sander -O -i mdin \**
> ? -o 6lyzwatmin1.out -p 6lyzwat.prmtop -c 6lyzwat.inpcrd \
> ? -r 6lyzwatmin1.rst -ref 6lyzwat.inpcrd*
>
> There is no error message, and when I check by keying in top, it gives me
>
>
>
> *10:56:50 up 8 days, 16:11, 10 users, load average: 0.91, 0.73, 0.35**
> 85 processes: 84 sleeping, 1 running, 0 zombie, 0 stopped
> 11:05:58 up 8 days, 16:21, 10 users, load average: 0.99, 0.83, 0.52
> 86 processes: 83 sleeping, 3 running, 0 zombie, 0 stopped
> CPU states: cpu user nice system irq softirq iowait idle
> total 50.2% 0.0% 0.0% 0.0% 0.0% 0.0% 49.7%
> cpu00 0.4% 0.0% 0.0% 0.0% 0.0% 0.0% 99.5%
> cpu01 100.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
> Mem: 16212488k av, 1276012k used, 14936476k free, 0k shrd, 172556k
> buff
> 349472k active, 426068k inactive
> Swap: 4096564k av, 0k used, 4096564k free 521588k
> cached*
>
> * PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME CPU COMMAND
> **
> 6401 qiuting 25 0 988 988 736 R 49.9 0.0 6:29 1 sander
> 6292 qiuting 15 0 18536 18M 13976 S 0.2 0.1 0:00 0 kdeinit
> 1 root 15 0 524 524 456 S 0.0 0.0 0:07 0 init
> 2 root RT 0 0 0 0 SW 0.0 0.0 0:00 0
> migration/0
> 3 root RT 0 0 0 0 SW 0.0 0.0 0:00 1
> migration/1*
>
> It seams sander is running, however, I can't see any output result in *6lyzwatmin1.out
> *even the job run for a long time.
>
> My input file is
>
> *6lyzwat: minimize solvent +ions**
> &cntrl
> imin =1,
> maxcyc =1000,
> ncyc =500,
> ntb =1,
> ntr=1,
> cut =12
> /
> Keep 6lyz frozen
> 500
> RES 1 129
> END
> END*
>
>
>
> I try in both amber8 and amber9, and I meet the same problem. Can somebody
> help me out?
>
>
>
> Thank you.
>
>
>
> Qiuting
>

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