Dear Ross Walker,
I try to get the output file by using one of my friends' single PC. The
output file is listed below. It seems that the way I form my ".inpcrd"and
".prmtop" file by modifing the Amber parameters cause the minimization
problem. Would you give me some suggestions?
ps: There are a platinum atom in my molecule. And that is why I have modify
the Amber parameters.
Thank you!
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
|Largest sphere to fit in unit cell has radius = 42.215
| New format PARM file being parsed.
| Version = 1.000 Date = 05/25/05 Time = 13:57:45
NATOM = 767 NTYPES = 26 NBONH = 278 MBONA = 548
NTHETH = 652 MTHETA = 846 NPHIH = 1262 MPHIA = 1492
NHPARM = 0 NPARM = 0 NNB = 4282 NRES = 25
NBONA = 548 NTHETA = 846 NPHIA = 1492 NUMBND = 47
NUMANG = 100 NPTRA = 52 NATYP = 31 NPHB = 24
IFBOX = 0 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 61986
| Hollerith 4629
| Integer 1555072
| Max Pairs 293761
| Max Rstack 57670
| Max Istack 3835
| Total 8189 kbytes
Found a non-zero 10-12 coefficient, but source
was not compiled with -DHAS_10_12.
If you are using a pre-1994 force field, you
will need to re-compile with this flag.
Sincerely,
Wendy
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: <amber.scripps.edu>
Sent: Tuesday, June 07, 2005 1:25 AM
Subject: RE: AMBER: fail of minimization in sander
> Hi Wendy,
>
> See if you can get an interactive shell on the cluster machine. Some
> systems
> let you do this. With pdb you do "qsub -i".
>
> If you want to check that your topology file is not corrupt you can run it
> through Amber's rdparm. This will give you an error if there are problems
> with the prmtop file. I doubt this is the problem though. Even if your Pt
> parameters were complete trash you'd still get some form of output. Just
> the
> results would be pretty meaningless.
>
> Also try redirecting standard out and standard error to a log file you can
> get at. E.g.
>
> /usr/local/bin/mpirun -np 4 sander -O \
> -i 1AIO-1D4-min.in -o 1AIO-1D4-min.out \
> -c 1AIO-1D4.inpcrd -p 1AIO-1D4.prmtop \
> -r 1AIO-1D4-min.rst < /dev/null >& 1AIO.log
>
> Some queue systems let you do this, other don't...
>
>> /usr/local/bin/wipe $hostlist
>
> I'm not sure what this command does? Is it possibly deleting any log files
> containing errors?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>> -----Original Message-----
>> From: owner-amber.scripps.edu
>> [mailto:owner-amber.scripps.edu] On Behalf Of wendy
>> Sent: 06 June 2005 09:13
>> To: amber.scripps.edu
>> Subject: Re: AMBER: fail of minimization in sander
>>
>> I have run the test file in Amber tutorial 1, and get normal
>> output file. I
>> don't have
>>
>> I am wondering if the Pt atom in my struture do something
>> wrong. I modified
>> the amber force field to make Xleap recongnize my Pt atom in
>> my structure.
>> How to check the validity of the ".protop" and ".inpcrd" file?
>>
>> I do not have licence to run Amber on my own computer. I am
>> using cluster
>> which is using LoadLeveler V3.2 for submitting jobs. My batch
>> file is listed
>> below.
>>
>> Thank you very much!
>>
>>
>> #!/bin/csh
>> # . job_type = parallel
>> # . node = 1
>> # . tasks_per_node = 4
>> # . class = q1n4g
>> # . node_usage = not_shared
>> # queue the program
>> # . queue
>> setenv hostlist hostlistfile
>> setenv K5MUTE 1
>> rm -f $hostlist
>> echo $LOADL_PROCESSOR_LIST > templist
>> awk '{gsub (/.itsc.cuhk.edu.hk/,"");print $1}' templist | tr
>> " " "\n" >
>> $hostlist
>> /usr/local/bin/wipe $hostlist
>> /usr/local/bin/lamboot $hostlist
>> /usr/local/bin/mpirun -np 4 sander -O -i 1AIO-1D4-min.in -o
>> 1AIO-1D4-min.out -c 1AIO-1D4.inpcrd -p 1AIO-1D4.prmtop -r
>> 1AIO-1D4-min.rst
>> < /dev
>> /null
>> /usr/local/bin/wipe $hostlist
>>
>>
>> ----- Original Message -----
>> From: "Bill Ross" <ross.cgl.ucsf.edu>
>> To: <amber.scripps.edu>
>> Sent: Monday, June 06, 2005 10:34 PM
>> Subject: Re: AMBER: fail of minimization in sander
>>
>>
>> >> I run sander in remote computer by sending the jobs by remote
>> >> logon. And I didn't find out batch output file.
>> >
>> > Have you run other programs this way? Is there normally a
>> > batch output file in such cases? What if you run it directly
>> > from the command line? Is there a core file?
>> >
>> > Bill
>> >
>> --------------------------------------------------------------
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>
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Received on Wed Jun 15 2005 - 09:53:00 PDT
