Maybe, i will try it, just want to figure out what the problem was.
No I am getting another error:
sander -O -i pbsa_com.in -o pbsa_com.2.out -c ./snapshot_com.crd.2 -p ./39798now.prmtop not successful
while napshot_com.crd.1 was processed ok.
Another thing is that I can get pdb from snapshot_com.crd.2 so prmtop fits to coordinates.
$AMBERHOME/exe/ambpdb -p 39798now.prmtop <snapshot_com.crd.2> 39798now.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/08/11 Time = 14:53:33
Just curious to get it working.
Best regards,
Andrew
11.05.2011, 00:14, "Jason Swails" <jason.swails.gmail.com>:
> It may be worth trying MMPBSA.py -- it automatically sets those parameters
> in most cases and has a good deal of error/redundancy checks.
>
> All the best,
> Jason
>
> 2011/5/10 Andrew Voronkov <drugdesign.yandex.ru>;
>
>> šHm, no actually it worked (btw it also works for ambpdb, it probably takes
>> šjust one of the snapshots) and has shown that there is difference of number
>> šof atoms between prmtop and crd, but the solution was super simple. I've
>> šjust used wrong ligand start and receptor start points.
>>
>> šBest regards,
>> šAndrew
>>
>> š08.05.2011, 22:10, "Bill Ross" <ross.cgl.ucsf.EDU>;:
>>>> šš[voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739now.prmtop \
>>>> šš<snapshot_com.crd.1> 36739-min1.pdb
>>> šAre you using an mdcrd file instead of a restrt? That won't work.
>>>
>>> šBill
>>>
>>> š_______________________________________________
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> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sun May 15 2011 - 09:30:02 PDT
