>> šsander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
>> š./39981.prmtop not successful
- this was error from mmpbsa_energy script run, i ve tested first snapshot with ambpdb andgot problem about prmtop file and crd file coordinates mismatch.
The problem turned out to be with crd and prmtop files
[voronkov.t60-2 34139]$ $AMBERHOME/exe/ambpdb -p 34139now.prmtop <snapshot_com.crd.1> snapshot_com.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/08/11 Time = 14:45:17
ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 3908 3862
COULD NOT READ COORDINATES FROM RESTRT FILE
now have to resolve what additional atoms I have in prmtop file.
07.05.2011, 22:54, "Jason Swails" <jason.swails.gmail.com>:
> 2011/5/7 Andrew Voronkov <drugdesign.yandex.ru>;
>
>> šYes, sure, just copied wrong line, but anyway with that line seems like
>> šthere is no problems, nothing is reported. But I get an error it when run
>> šmmpbsa_energy.pl script:
>>
>> šsander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
>> š./39981.prmtop not successful
>
> It appears as though this is the full command you're trying to enter. šThus,
> it is parsing "not" as a flag, which it doesn't recognize. šTake out "not
> successful" and rerun it.
>
>> šhere is the log, looks normal:
>>
>> š=>> Init data
>> ššššPresuming executables of amber suite to be in
>> š/home/osolodkin/amber10/exe
>>
>> š=>> Reading input parameters
>> ššššFound PREFIX => snapshot
>> ššššFound PATH => ./
>> ššššFound COMPLEX => 1
>> ššššFound RECEPTOR => 1
>> ššššFound LIGAND => 1
>> ššššFound COMPT => ./39981.prmtop
>> ššššFound RECPT => ./1ijynow.prmtop
>> ššššFound LIGPT => ./39981g.prmtop
>> ššššFound GC => 0
>> ššššFound AS => 0
>> ššššFound DC => 0
>> ššššFound MM => 1
>> ššššFound GB => 1
>> ššššFound PB => 1
>> ššššFound MS => 1
>> ššššFound NM => 0
>> ššššFound PROC => 2
>> ššššFound REFE => 0
>> ššššFound INDI => 1.0
>> ššššFound EXDI => 80.0
>> ššššFound SCALE => 2
>> ššššFound LINIT => 1000
>> ššššFound PRBRAD => 1.4
>> ššššFound ISTRNG => 0.0
>> ššššFound RADIOPT => 0
>> ššššFound NPOPT => 1
>> ššššFound CAVITY_SURFTEN => 0.0072
>> ššššFound CAVITY_OFFSET => 0.00
>> ššššFound SURFTEN => 0.0072
>> ššššFound SURFOFF => 0.00
>> ššššFound DIELC => 1.0
>> ššššFound IGB => 2
>> ššššFound GBSA => 1
>> ššššFound SALTCON => 0.00
>> ššššFound EXTDIEL => 80.0
>> ššššFound INTDIEL => 1.0
>> ššššFound SURFTEN => 0.0072
>> ššššFound SURFOFF => 0.00
>> ššššFound PROBE => 0.0
>>
>> š=>> Checking sanity
>> ššššChecking GENERAL
>> ššššSetting START to default 1
>> ššššSetting STOP to default 10e10
>> ššššSetting OFFSET to default 1
>> ššššSetting VERBOSE to default 0
>> ššššChecking MM
>> ššššChecking PB
>> ššššChecking GB
>> ššššChecking MS
>>
>> š=>> Creating input
>> ššššSander input
>> ššššPBSA input
>>
>> š=>> Calculating energy / entropy contributions
>> ššššCalc contrib for ./snapshot_com.crd.1
>> ššššššššCalc MM/GB/SAS
>
> What's the problem here?
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Sun May 08 2011 - 07:00:03 PDT
