AMBER Archive (2008)

Subject: Re: AMBER: problem in starting sander

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jun 08 2008 - 23:36:32 CDT

did the test cases all pass?

On Sun, Jun 8, 2008 at 10:40 PM, Qiuting Hong <qiutinghong_at_gmail.com> wrote:
> 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
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu