What confuses me is that there is the difference in number of atoms between coordinates atoms from snapshots, but no difference with coordinates in rst file resulted from molecular dynamics from mdrcd trajectory. So something is wrong with parametrization of protein-ligand complex without solvent, some difference of it with number of atoms in the sanpshots.
[voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739now.prmtop <snapshot_com.crd.1> 36739-min1.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/08/11 Time = 14:47:26
ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 3911 3862
COULD NOT READ COORDINATES FROM RESTRT FILE
[voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739.prmtop <36739_md1.rst> 36739_md1.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 01/28/10 Time = 16:41:20
[voronkov.t60-2 36739]$
Best regards,
Andrew
08.05.2011, 17:57, "Andrew Voronkov" <drugdesign.yandex.ru>:
>>> ššsander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
>>> šš./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 = ššš1.000 Date = 05/08/11 Time = 14:45:17
>
> ššATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES ššš3908 ššš3862
> 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>;:
>
>> š2011/5/7 Andrew Voronkov <drugdesign.yandex.ru>;;
>>> ššYes, sure, just copied wrong line, but anyway with that line seems like
>>> ššthere is no problems, nothing is reported. But I get an error it when run
>>> ššmmpbsa_energy.pl script:
>>>
>>> ššsander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
>>> šš./39981.prmtop not successful
>> šIt appears as though this is the full command you're trying to enter. šThus,
>> šit is parsing "not" as a flag, which it doesn't recognize. šTake out "not
>> šsuccessful" and rerun it.
>>> ššhere is the log, looks normal:
>>>
>>> šš=>> Init data
>>> šššššPresuming executables of amber suite to be in
>>> šš/home/osolodkin/amber10/exe
>>>
>>> šš=>> Reading input parameters
>>> šššššFound PREFIX => snapshot
>>> šššššFound PATH => ./
>>> šššššFound COMPLEX => 1
>>> šššššFound RECEPTOR => 1
>>> šššššFound LIGAND => 1
>>> šššššFound COMPT => ./39981.prmtop
>>> šššššFound RECPT => ./1ijynow.prmtop
>>> šššššFound LIGPT => ./39981g.prmtop
>>> šššššFound GC => 0
>>> šššššFound AS => 0
>>> šššššFound DC => 0
>>> šššššFound MM => 1
>>> šššššFound GB => 1
>>> šššššFound PB => 1
>>> šššššFound MS => 1
>>> šššššFound NM => 0
>>> šššššFound PROC => 2
>>> šššššFound REFE => 0
>>> šššššFound INDI => 1.0
>>> šššššFound EXDI => 80.0
>>> šššššFound SCALE => 2
>>> šššššFound LINIT => 1000
>>> šššššFound PRBRAD => 1.4
>>> šššššFound ISTRNG => 0.0
>>> šššššFound RADIOPT => 0
>>> šššššFound NPOPT => 1
>>> šššššFound CAVITY_SURFTEN => 0.0072
>>> šššššFound CAVITY_OFFSET => 0.00
>>> šššššFound SURFTEN => 0.0072
>>> šššššFound SURFOFF => 0.00
>>> šššššFound DIELC => 1.0
>>> šššššFound IGB => 2
>>> šššššFound GBSA => 1
>>> šššššFound SALTCON => 0.00
>>> šššššFound EXTDIEL => 80.0
>>> šššššFound INTDIEL => 1.0
>>> šššššFound SURFTEN => 0.0072
>>> šššššFound SURFOFF => 0.00
>>> šššššFound PROBE => 0.0
>>>
>>> šš=>> Checking sanity
>>> šššššChecking GENERAL
>>> šššššSetting START to default 1
>>> šššššSetting STOP to default 10e10
>>> šššššSetting OFFSET to default 1
>>> šššššSetting VERBOSE to default 0
>>> šššššChecking MM
>>> šššššChecking PB
>>> šššššChecking GB
>>> šššššChecking MS
>>>
>>> šš=>> Creating input
>>> šššššSander input
>>> šššššPBSA input
>>>
>>> šš=>> Calculating energy / entropy contributions
>>> šššššCalc contrib for ./snapshot_com.crd.1
>>> šššššššššCalc MM/GB/SAS
>> šWhat's the problem here?
>>
>> šHTH,
>> šJason
>>
>> š--
>> šJason M. Swails
>> šQuantum Theory Project,
>> šUniversity of Florida
>> šPh.D. Candidate
>> š352-392-4032
>> š_______________________________________________
>> šAMBER mailing list
>> šAMBER.ambermd.org
>> šhttp://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun May 08 2011 - 08:30:03 PDT
