snap:
#Generate snapshots
.GENERAL
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../com.top
RECPT ../rec.top
LIGPT ../lig.top
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
#
.MAKECRD
BOX YES
NTOTAL 47015
NSTART 1
NSTOP 1000
NFREQ 10
#
NUMBER_LIG_GROUPS 1
LSTART 6707
LSTOP 6733
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 6706
#
.TRAJECTORY
TRAJECTORY ../../rst/md1.rst
------------------------------------------------------------
bind:
.GENERAL
PREFIX snapshot
PATH ../snap1/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../com.top
RECPT ../rec.top
LIGPT ../lig.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 1
#
NM 0
#
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 3
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
#
.MS
PROBE 0.0
-----------------------------------------------------
snapshot_com.all.out :
MM
PB
MS
PB_SURFTEN 0.0072
PB_SURFOFF 0.00
1
BOND = 5527.7282 ANGLE = 3549.8797 DIHED =
4572.4897
VDWAALS = -3299.2570 EEL = -24133.5090 HBOND =
0.0000
1-4 VDW = 1522.5552 1-4 EEL = 17390.0677 RESTRAINT =
0.0000
corrected reaction field energy: -14225.509919
surface area = 21291.846
ECAVITY = 21291.846
EDISPER = 0.0000
2
BOND = 5611.7242 ANGLE = 3540.7968 DIHED =
4619.9158
VDWAALS = -3305.0051 EEL = -24225.6943 HBOND =
0.0000
1-4 VDW = 1535.7690 1-4 EEL = 17352.0963 RESTRAINT =
0.0000
corrected reaction field energy: -14156.988741
surface area = 21545.567
ECAVITY = 21545.567
EDISPER = 0.0000
3
BOND = 4998.5208 ANGLE = 3531.3218 DIHED =
4624.3629
VDWAALS = -3291.2172 EEL = -24219.7381 HBOND =
0.0000
1-4 VDW = 1542.0590 1-4 EEL = 17392.9788 RESTRAINT =
0.0000
corrected reaction field energy: -14234.833418
surface area = 21916.489
ECAVITY = 21916.489
EDISPER = 0.0000
4
BOND = 6991.5351 ANGLE = 3641.5053 DIHED =
4572.9531
VDWAALS = -3296.2592 EEL = -24393.0952 HBOND =
0.0000
1-4 VDW = 1519.4070 1-4 EEL = 17410.9097 RESTRAINT =
0.0000
corrected reaction field energy: -13952.250701
surface area = 21664.640
ECAVITY = 21664.640
EDISPER = 0.0000
5
BOND = 6940.7391 ANGLE = 3642.5870 DIHED =
4564.7746
VDWAALS = -3299.1843 EEL = -24230.0725 HBOND =
0.0000
1-4 VDW = 1538.1436 1-4 EEL = 17368.4994 RESTRAINT =
0.0000
corrected reaction field energy: -14053.602574
surface area = 21557.437
ECAVITY = 21557.437
EDISPER = 0.0000
6
BOND = 7215.2873 ANGLE = 3672.7766 DIHED =
4568.3137
VDWAALS = -3314.8553 EEL = -24275.1713 HBOND =
0.0000
1-4 VDW = 1555.6592 1-4 EEL = 17391.5978 RESTRAINT =
0.0000
corrected reaction field energy: -13898.868551
surface area = 21627.317
ECAVITY = 21627.317
EDISPER = 0.0000
7
BOND = 6904.6747 ANGLE = 3632.9319 DIHED =
4570.6171
VDWAALS = -3295.2435 EEL = -24241.0596 HBOND =
0.0000
1-4 VDW = 1524.1689 1-4 EEL = 17403.3138 RESTRAINT =
0.0000
corrected reaction field energy: -14012.598300
surface area = 21864.893
ECAVITY = 21864.893
EDISPER = 0.0000
8
BOND = 6572.0523 ANGLE = 3666.1718 DIHED =
4578.6093
VDWAALS = -3290.7906 EEL = -24347.6482 HBOND =
0.0000
1-4 VDW = 1513.1670 1-4 EEL = 17378.5779 RESTRAINT =
0.0000
corrected reaction field energy: -13954.055682
surface area = 21868.032
ECAVITY = 21868.032
-------------------------------------------------------------
amber10 with mm_pbsa.pl
I found the "BOND" in sanpshot_com.all.out file varied greatly....from 5000
to 10000....
2010/12/6 Ray Luo, Ph.D. <ray.luo.uci.edu>
> Can you share with us your mmpba input file and which version of amber you
> are using?
>
> Ray
>
> On Sun, Dec 5, 2010 at 7:12 PM, Alice Wang <compu.chem.w.gmail.com> wrote:
>
> > Thank you Jason
> > I checked the *out file, the number is ok
> > but when I check the mm_pbsa.log, I found the warning, as blew, is it the
> > reason? how to solve it ? Thanks it again.
> >
> > =>> 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 PBCAV for PB in 88 -> Taken from 87
> > WARNING: Missing PBDIS for PB in 88 -> Taken from 87
> > WARNING: Missing SURF for MS in 88 -> Taken from 87
> > Reading snapshot_rec.all.out
> > Checking consistency of CALC
> > Checking consistency of DATA
> > Reading snapshot_lig.all.out
> > Checking consistency of CALC
> > Checking consistency of DATA
> >
> >
> >
> > 2010/12/6 Jason Swails <jason.swails.gmail.com>
> >
> > > Look at the temporary output files created by sander and see if the
> > numbers
> > > make sense. Depending on the version of mm_pbsa that you're using,
> > either
> > > pbsa_com.#.out, pbsa_rec.#.out, pbsa_lig.#.out (for amber10/amber11, I
> > > think) and sander_com.#.out, etc.
> > >
> > > Make sure you set VERBOSE to a proper setting so that it keeps all of
> the
> > > files. See the amber manual for a more detailed discussion.
> > >
> > > All the best,
> > > Jason
> > >
> > > On Sun, Dec 5, 2010 at 9:26 PM, Alice Wang <compu.chem.w.gmail.com>
> > wrote:
> > >
> > > > Dear Amber,
> > > >
> > > > My pbsa out put file is blow:
> > > > # COMPLEX RECEPTOR
> > > > LIGAND
> > > > # ----------------------- -----------------------
> > > > -----------------------
> > > > # MEAN STD MEAN STD
> > > > MEAN STD
> > > > # ======================= =======================
> > > > =======================
> > > > ELE -6803.94 114.19 -6670.34 114.97
> > > > -101.61 1.59
> > > > VDW -1772.99 26.24 -1734.65 26.33
> > > > 5.04 1.38
> > > > INT 16439.74 2118.23 16405.28 2118.61
> > > > 34.47 3.69
> > > > GAS 7862.82 2103.51 8000.29 2101.62
> > > > -62.10 3.76
> > > > PBSUR 157.30 1.27 158.36 1.29
> > > > 3.21 0.02
> > > > PBCAL -8491.30 115.80 -8517.82 116.78
> > > > -20.24 1.30
> > > > PBSOL -8333.99 115.33 -8359.46 116.33
> > > > -17.03 1.30
> > > > PBELE -15295.23 43.75 -15188.16 43.63
> > > > -121.85 1.32
> > > > PBTOT -471.17 2106.88 -359.17 2106.46
> > > > -79.13 3.67
> > > >
> > > > # DELTA
> > > > # -----------------------
> > > > # MEAN STD
> > > > # =======================
> > > > ELE -31.99 3.11
> > > > VDW -43.38 2.20
> > > > INT -0.00 0.00
> > > > GAS -75.37 3.88
> > > > PBSUR -4.26 0.21
> > > > PBCAL 46.76 3.32
> > > > PBSOL 42.50 3.36
> > > > PBELE 14.77 2.58
> > > > PBTOT -32.87 3.02
> > > >
> > > > The STD value is high in the PBTOT of complex, receptor.
> > > >
> > > > Is it wrong?
> > > >
> > > > Thanks !
> > > >
> > > > Alice Wang
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 05 2010 - 23:30:03 PST
