Yes, sure, just copied wrong line, but anyway with that line seems like there is no problems, nothing is reported. But I get an error it when run mmpbsa_energy.pl script:
sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./39981.prmtop not successful
here is the log, looks normal:
=>> Init data
Presuming executables of amber suite to be in /home/osolodkin/amber10/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./39981.prmtop
Found RECPT => ./1ijynow.prmtop
Found LIGPT => ./39981g.prmtop
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
Found PROC => 2
Found REFE => 0
Found INDI => 1.0
Found EXDI => 80.0
Found SCALE => 2
Found LINIT => 1000
Found PRBRAD => 1.4
Found ISTRNG => 0.0
Found RADIOPT => 0
Found NPOPT => 1
Found CAVITY_SURFTEN => 0.0072
Found CAVITY_OFFSET => 0.00
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 0.0
=>> Checking sanity
Checking GENERAL
Setting START to default 1
Setting STOP to default 10e10
Setting OFFSET to default 1
Setting VERBOSE to default 0
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
=>> Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Calc MM/GB/SAS
24.04.2011, 18:54, "Bill Miller III" <brmilleriii.gmail.com>:
> When you used the command line:
>
> sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
> ./37578.prmtop not successful
>
> you left the "not successful" at the end. Sander thought that "not" was a
> flag you were trying to use, but obviously this isn't a proper flag. Drop
> the "not successful" from the end of the command line argument and try
> again.
>
> -Bill
>
> On Sun, Apr 24, 2011 at 10:07 AM, Andrew Voronkov <drugdesign.yandex.ru>;wrote:
>
>> šDear Amber users, I have tried to use mmpbsa.pl šand I have got the next
>> šerrors:
>>
>> š" $AMBERHOME/exe/mm_pbsa.pl 37578_energy.mmpbsa > 37578_energy.log
>> šššššššš/home/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c
>> š./snapshot_com.crd.1 -p ./37578.prmtop not successful"
>>
>> šThen I have tried to do it directly without mmpsa.pl script and got the
>> šerror below which is not listed in Amber archive. What does it mean, flag
>> š"not"?
>>
>> š[voronkov.t60-2 37578]$ sander -O -i sander_com.in -o sander_com.1.out -c
>> š./snapshot_com.crd.1 -p ./37578.prmtop not successful
>>
>> šššššmdfil: Error unknown flag: not
>>
>> šššššusage: sander š[-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
>> ššššššššššššššššššš[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
>> šrstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
>> š-radii radii -y inptraj]
>> šConsult the manual for additional options.
>>
>> šSincerely yours,
>> šAndrey
>>
>> š_______________________________________________
>> šAMBER mailing list
>> šAMBER.ambermd.org
>> šhttp://lists.ambermd.org/mailman/listinfo/amber
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat May 07 2011 - 11:30:03 PDT
