I have used Amber10 for MD run and further calculations. I am using perl scripts for mmpbsa.INPUT files
for extraction of coordinates as follows:
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT
../prmtop/complex_vac.prmtop
RECPT ../prmtop/prot_vac.prmtop
LIGPT ../prmtop/BIM.prmtop
GC 1
AS 0
DC 0
MM 0
GB
0
PB 0
MS 0
NM 0
.MAKECRD
BOX YES
NTOTAL 9249
NSTART 1
NSTOP 999
NFREQ
100
NUMBER_LIG_GROUPS 1
LSTART 9188
LSTOP 9249
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 9187
.TRAJECTORY
TRAJECTORY ../strip_mdcrd/2mBIM_nowat.mdcrd
.PROGRAMS
for binding energy calculation:
.GENERAL
PREFIX
snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../prmtop/complex_vac.prmtop
RECPT ../prmtop/prot_vac.prmtop
LIGPT ../prmtop/BIM.prmtop
#
GC
0
AS 0
DC 0
#
MM 1
GB 1
PB 1
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
.
Extraction occurs with no problems but after running binding energy script it gives error as follows:
/opt/amber10/exe/sander
-O -i pbsa_com.in -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p
../prmtop/complex_vac.prmtop not successful
log file of binding energy calculation:
=>> Init data
Presuming executables of amber suite to be in /opt/amber10/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ../prmtop/complex_vac.prmtop
Found RECPT =>
../prmtop/prot_vac.prmtop
Found LIGPT => ../prmtop/BIM.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
Generate PDB
Center PDB
Calc PBSA
pbsa_com.1.out:
File Assignments:
| MDIN: pbsa_com.in
| MDOUT: pbsa_com.1.out
|INPCRD:
./snapshot_com.crd.1
| PARM: ../prmtop/complex_vac.prmtop
|RESTRT:
restrt
| REFC: refc
| MDVEL:
mdvel
| MDEN: mden
| MDCRD:
mdcrd
|MDINFO: mdinfo
|INPDIP:
inpdip
|RSTDIP: rstdip
Here is the input file:
File generated by mm_pbsa.pl. Using
PB
&cntrl
ntf = 1, ntb =
0,
igb = 10, dielc = 1.0,
cut = 999.0, nsnb =
99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 0, ntmin = 2,
ivcap =
0, cutcap = -1,
xcap = 0, ycap = 0, zcap = 0
idecomp=
0,
&end
&pb
epsin = 1.0, epsout = 80.0,
istrng = 0.0, radiopt =
0,
sprob = 1.4, space = 0.5,
maxitn = 1000, npopt = 1, dbfopt = 1,
cavity_surften = 0.0072, fillratio = 4.00,
cavity_offset = 0.00,
npbverb= 1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 08/09/11 Time = 22:39:42
NATOM = 9249 NTYPES = 18 NBONH = 4578 MBONA = 4783
NTHETH =
10490 MTHETA = 6457 NPHIH = 19824 MPHIA = 15978
NHPARM = 0 NPARM = 0 NNB = 51187 NRES = 579
NBONA = 4783 NTHETA = 6457 NPHIA = 15978 NUMBND = 66
NUMANG = 132 NPTRA = 49 NATYP = 47 NPHB = 0
IFBOX = 0 NMXRS = 62 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii
(mbondi)
| Memory Use Allocated
| Real 592745
| Hollerith 56075
| Integer 500704
| Max Pairs 1
| nblistReal
0
| nblist Int 0
| Total 6805 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE
RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx
= 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf
= 1, ntb = 0, igb = 10, nsnb = 99999
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc
= 0, ncyc = 10, ntmin = 2
dx0 = 0.01000, drms = 0.00010
======== Implicit Solvent Initialization ========
Max Nonbonded Pairs: 10405125 2247507 42772001
no. of atoms processed in PB initialization: 9249
NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
1 LYS N N3 0.096600 0.746100 0.862600 1.550000 1.550000
2 LYS H1 H 0.216500
0.000000 0.000000 1.300000 1.300000
3 LYS H2 H 0.216500 0.000000 0.000000 1.300000 1.300000
4 LYS H3 H 0.216500 0.000000 0.000000 1.300000 1.300000
5 LYS CA CT -0.001500 0.116500 1.661800 1.700000 1.700000
6 LYS HA HP 0.118000 0.000000 0.000000 1.300000 1.300000
7 LYS CB CT 0.021200 0.077800 0.213700 1.700000 1.700000
8 LYS HB2 HC 0.028300 0.000000
0.000000 1.300000 1.300000
.
.
.
246 BIM C20 ca -0.101600 0.043300 -0.012800 1.700000 1.700000
9247 BIM H12 ha 0.144900 0.144900 0.144900 1.300000 1.300000
9248 BIM C21 ca -0.191300 -0.065000 -0.108300 1.700000 1.700000
9249 BIM H13 ha 0.126300 0.126300 0.126300 1.300000 1.300000
total system charges (+/-) for PB -2.9998 1123.8366 -1126.8364
cavity_surften = 0.0072 cavity_offset =
0.0000
SAS Surface: surface dots generated: 366
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found:
0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NB-update: residue-based nb list 4087009
NB-update: atom-based nb list 905095
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 67.500 73.000 67.500
Xmin, Xmax, Xmax-Xmin: 20.518 114.427 93.909
Ymin, Ymax, Ymax-Ymin: 17.394 128.517 111.123
Zmin, Zmax, Zmax-Zmin: 26.562 108.482 81.920
beginning box center at level 1
67.500 73.000 67.500
beginning box center at level 2 67.500 73.000 67.500
Grid dimension at level 1 95 113 83
Grid origin corrected at level 1 -124.500 -155.000 -100.500
Grid dimension at level 2 203 237 179
Grid origin corrected at level 2 16.500 13.500 22.500
SA surface: setting up working radii
SA surface: found nonzero radii 9249
Number of SA srf points exposed133796
SA Bomb in sa_arc(): Allocation
aborted 0 0 0
0 41
I
tried same process by removing calcium zinc ions which are present in
respective system but error remains the same. I also tried considering
ions as ligand, as receptor but no positive result. I also reduced the
protein size by abducting regulatory domain and keeping only active
domain but I could not form the neccessary topology files as removal of
part of protein cause imbalance of hydrogens due to loss of peptide
bond. tleap adds some extra hydrogens on its own but they are not
present in original mdcrd trjectory file so i could not use such
topology files for calculations.
Than you so much for your consideration.
Regards,
Jyotsna
--- On Mon, 5/7/12, Jason Swails <jason.swails.gmail.com> wrote:
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] MMPBSA calculation of large proteins
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Monday, May 7, 2012, 2:14 PM
We need more information.
What version of Amber/AmberTools are you using? Which MM/PBSA script are
you using? What is your input file? What is your *exact* error (not just
part of your error). Based on the provided information it's impossible to
debug any further.
All the best,
Jason
On Mon, May 7, 2012 at 2:58 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
> Dear AMBER users,
> I am trying to run MMPBSA script on 10 ns simulation trajectory.( My
> protein-ligand complex system has 579 residues. It is a multidomain
> protein; active domain and regulatory domain are situated far away from
> each other, but linked by a large loop. Ligand is present in an active
> domain). Extraction of coordinates is done successfully but during binding
> energy calculation job gets aborted at first coordinate only with the error
> "complex_vac.prmtop not successful".I have tried the adjustment with
> fillratio (2,3 or 4) but it didn't help. Waiting for suggestions
> Thank you.Jyotsna
>
> _______________________________________________
> 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 May 07 2012 - 10:00:04 PDT
