Look at folder permissions to make sure that you can actually read and
create files in whatever directory you're trying to use.
Also, consider using MMPBSA.py from AmberTools 1.5. It can be downloaded
freely, and only requires Amber 11 for decomposition analysis and QM/MMGBSA
calculations.
HTH,
Jason
On Mon, Jul 18, 2011 at 1:01 AM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Jason,
> Thanks for your comments. I am trying to compare GBSA calculations through
> mm_pbsa.pl using Amber 8 and Amber10. I have used the same amber8 input
> script to perform GBSA calculations using amber10. The script is
> generating all the files expect snapshot_statistics.out. I am getting the
> following in the .log file
>
> Calc contrib for ./snapshot_lig.crd.25
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Generate PQR
> Calc MS
>
> =>> Doing statistics
> =>> Values of global variables
> TEMP = 300
> R = 8.314
> gammaP = 0.00542
> betaP = 0.92
> gammaG = 0.0072
> betaG = 0.00
> =>> Reading input
> =>> Reordering files
> Final order:
> 1. snapshot_com.all.out: -
> 2. snapshot_rec.all.out: -
> 3. snapshot_lig.all.out: -
> =>> Reading files
> Reading snapshot_com.all.out
> WARNING: Missing SROT for NM in 0 -> Taken from -1
> WARNING: Missing STOT for NM in 0 -> Taken from -1
> WARNING: Missing STRA for NM in 0 -> Taken from -1
> WARNING: Missing SVIB for NM in 0 -> Taken from -1
> WARNING: Missing SROT for NM in 1 -> Taken from 0
> WARNING: Missing STOT for NM in 1 -> Taken from 0
> WARNING: Missing STRA for NM in 1 -> Taken from 0
> WARNING: Missing SVIB for NM in 1 -> Taken from 0
> WARNING: Missing SROT for NM in 2 -> Taken from 1
> WARNING: Missing STOT for NM in 2 -> Taken from 1
> WARNING: Missing STRA for NM in 2 -> Taken from 1
> WARNING: Missing SVIB for NM in 2 -> Taken from 1
> WARNING: Missing SROT for NM in 3 -> Taken from 2
> WARNING: Missing STOT for NM in 3 -> Taken from 2
> WARNING: Missing STRA for NM in 3 -> Taken from 2
> WARNING: Missing SVIB for NM in 3 -> Taken from 2
> WARNING: Missing SROT for NM in 4 -> Taken from 3
> WARNING: Missing STOT for NM in 4 -> Taken from 3
> WARNING: Missing STRA for NM in 4 -> Taken from 3
>
>
>
>
>
> WARNING: Missing STRA for NM in 98 -> Taken from 97
> WARNING: Missing SVIB for NM in 98 -> Taken from 97
> WARNING: Missing SROT for NM in 99 -> Taken from 98
> WARNING: Missing STOT for NM in 99 -> Taken from 98
> WARNING: Missing STRA for NM in 99 -> Taken from 98
> WARNING: Missing SVIB for NM in 99 -> Taken from 98
> WARNING: Missing SROT for NM in 100 -> Taken from 99
> WARNING: Missing STOT for NM in 100 -> Taken from 99
> WARNING: Missing STRA for NM in 100 -> Taken from 99
> WARNING: Missing SVIB for NM in 100 -> Taken from 99
> WARNING: Missing SROT for NM in 101 -> Taken from 100
> WARNING: Missing STOT for NM in 101 -> Taken from 100
> WARNING: Missing STRA for NM in 101 -> Taken from 100
> WARNING: Missing SVIB for NM in 101 -> Taken from 100
> Reading snapshot_rec.all.out
> Checking CALC
>
> and also
> Talon-login[115] mhb75$ less test11.e120494
> Calc mode NM not found
> Permission denied.
>
> This is my input file:
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./hAChE.prmtop
> RECPT ./hAChE-sarin.prmtop
> LIGPT ./MMB.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 0
> MS 1
> NM 0
> .PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> SURFTEN 0.0072
> SURFOFF 0.00
> .MM
> DIELC 1.0
> .GB
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> SURFTEN 0.0072
> SURFOFF 0.00
> .MS
> PROBE 0.0
> .PROGRAMS
>
>
>
> I have made NM==0, and I don't understand why it is complaining about NM?
> Any suggestions?
>
> mani
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 18 2011 - 08:00:03 PDT
