I ran tleap, using the commands,
$tleap -s -f input_prpe.txt
which had the follwing lines.
---------
source /usr/soft/amber12/dat/leap/cmd/leaprc.ff13
Verbosity 2
logFile tleap_log.txt
Receptor = loadPdb model3.pdb
saveAmberparm Receptor model3_noion.top model3_noion.crd
addIons Receptor Cl- 0
saveAmberparm Receptor model3_ion.top model3_ion.crd
solvateoct Receptor TIP3PBOX 12.0
saveamberparm Receptor model3-wat.top model3-wat.crd.
thank you
Bergy
On 3/19/14, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Mar 19, 2014 at 11:55 AM, BERGY <nucleic81.gmail.com> wrote:
>
>> Dear all,
>>
>> I get the following msg on submitting my job. all amber 12 and
>> ambertools 13 update are done.
>> ---------------------
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>> rank 0 in job 4 mambo_42345 caused collective abort of all ranks
>> exit status of rank 0: killed by signal 9
>> -------------------
>> The OUT file has the following error msg.
>>
>>
>> | Largest sphere to fit in unit cell has radius = 33.861
>>
>> | New format PARM file being parsed.
>> | Version = 1.000 Date = 03/19/14 Time = 03:20:35
>>
>> | Note: 1-4 EEL scale factors are being read from the topology file.
>>
>> | Note: 1-4 VDW scale factors are being read from the topology file.
>> CUDA (GPU): Prmtop appears to contain modified off-diagonal elements
>> for VDW A coef.
>> GPU code does NOT support such force field modifications.
>> Found Aij = 787979.7920942737 expected
>> 479622.7030000000
>> i = 20 j = 1 Matrix element = 191
>>
>> Thanking you
>>
>
> How did you make your topology file?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Mar 20 2014 - 03:00:03 PDT
