Yes, the message in pbsa_lig.77.out also indicates about fillratio.
How to go about this and where exactly should I include the fillratio?
Here is the out file:
pbsa_lig.77.out
-------------------------------------------------------
Amber 9 PBSA Scripps/UCSF 2006
-------------------------------------------------------
| Run on 09/18/2014 at 19:20:32
[-O]verwriting output
File Assignments:
| MDIN: pbsa.in
| MDOUT:
pbsa_lig.77.out
|INPCRD:
./snapshot_lig.crd.77
| PARM:
./lig_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,
&end
&pb
epsin = 1.0, epsout =
80.0,
istrng = 0, radiopt =
0,
sprob = 1.4, space =
0.5,
maxitn = 1000, npopt =
1,
cavity_surften = 0.0072, cavity_offset =
0.00,
npbverb=
1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 05/25/10 Time = 12:37:34
NATOM = 90 NTYPES = 7 NBONH = 38 MBONA = 60
NTHETH = 76 MTHETA = 88 NPHIH = 142 MPHIA = 144
NHPARM = 0 NPARM = 0 NNB = 486 NRES = 1
NBONA = 60 NTHETA = 88 NPHIA = 144 NUMBND = 19
NUMANG = 36 NPTRA = 9 NATYP = 11 NPHB = 0
IFBOX = 0 NMXRS = 90 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 3395
| Hollerith 543
| Integer 24315
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 123 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
LIG
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: 4051 4051 4051
no. of atoms processed in PB initialization: 90
NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
1 LIG C cc -0.123000 0.044000 0.045000 1.700000 1.700000
2 LIG C1 cd -0.257600 -0.091600 0.468300 1.700000 1.700000
3 LIG C2 cd 0.515900 0.515900 -0.394800 1.700000 1.700000
4 LIG N nc -0.619300 -0.619300 -0.010800 1.550000 1.550000
5 LIG C3 cf 0.081600 0.081600 0.135300 1.700000 1.700000
6 LIG C4 cc 0.092600 0.092600 -0.401100 1.700000 1.700000
7 LIG C5 cd -0.086100 -0.086100 0.268100 1.700000 1.700000
8 LIG C6 cc -0.146000 0.019000 -0.048100 1.700000 1.700000
9 LIG N1 na -0.089100 0.253600 0.081400 1.550000 1.550000
10 LIG C7 cc -0.146000 0.019000 -0.048100 1.700000 1.700000
11 LIG C8 cd -0.086100 -0.086100 0.268100 1.700000 1.700000
12 LIG H hn 0.342700 0.342700 0.342700 1.300000 1.300000
13 LIG C9 cf 0.081600 0.081600 0.135300 1.700000 1.700000
14 LIG C10 cc 0.092600 0.092600 -0.401100 1.700000 1.700000
15 LIG C11 cc -0.123000 0.044000 0.045000 1.700000 1.700000
16 LIG N2 nc -0.619300 -0.619300 -0.010800 1.550000 1.550000
17 LIG C12 cd -0.257600 -0.091600 0.468300 1.700000 1.700000
18 LIG C13 cd 0.515900 0.515900 -0.394800 1.700000 1.700000
19 LIG C14 cf -0.199800 -0.199800 0.508000 1.700000 1.700000
20 LIG C15 cd 0.098900 0.098900 0.081700 1.700000 1.700000
21 LIG C16 cc -0.123000 0.058000 0.214900 1.700000 1.700000
22 LIG N3 na -0.229100 0.124600 0.322400 1.550000 1.550000
23 LIG C17 cc -0.123000 0.058000 0.214900 1.700000 1.700000
24 LIG C18 cd 0.098900 0.098900 0.081700 1.700000 1.700000
25 LIG H1 hn 0.353700 0.353700 0.353700 1.300000 1.300000
26 LIG C19 cf -0.199800 -0.199800 0.508000 1.700000 1.700000
27 LIG C20 ca 0.047200 0.047200 0.277800 1.700000 1.700000
28 LIG C21 ca -0.131000 0.075000 0.324900 1.700000 1.700000
29 LIG C22 ca -0.023300 0.202700 0.325600 1.700000 1.700000
30 LIG N4 na 0.047900 0.047900 0.755000 1.550000 1.550000
31 LIG C23 ca -0.023300 0.201700 0.323600 1.700000 1.700000
32 LIG C24 c3 -0.042400 0.302700 0.350600 1.700000 1.700000
33 LIG C25 ca -0.132000 0.074000 0.322900 1.700000 1.700000
34 LIG C26 cc 0.093000 0.093000 0.000200 1.700000 1.700000
35 LIG C27 cc -0.143000 0.059000 0.459000 1.700000 1.700000
36 LIG C28 cd 0.084000 0.307000 0.018800 1.700000 1.700000
37 LIG N5 na -0.347200 -0.347200 0.748000 1.550000 1.550000
38 LIG C29 cd 0.087000 0.310000 0.010800 1.700000 1.700000
39 LIG C30 c3 0.137100 0.478200 0.131000 1.700000 1.700000
40 LIG C31 cc -0.151000 0.048000 0.451000 1.700000 1.700000
41 LIG C32 ca 0.047200 0.047200 0.277800 1.700000 1.700000
42 LIG C33 ca -0.131000 0.075000 0.324900 1.700000 1.700000
43 LIG C34 ca -0.023300 0.202700 0.325600 1.700000 1.700000
44 LIG N6 na 0.047900 0.047900 0.755000 1.550000 1.550000
45 LIG C35 ca -0.023300 0.201700 0.323600 1.700000 1.700000
46 LIG C36 c3 -0.042400 0.302700 0.350600 1.700000 1.700000
47 LIG C37 ca -0.132000 0.074000 0.322900 1.700000 1.700000
48 LIG C38 cc 0.093000 0.093000 0.000200 1.700000 1.700000
49 LIG C39 cc -0.151000 0.048000 0.451000 1.700000 1.700000
50 LIG C40 cd 0.087000 0.310000 0.010800 1.700000 1.700000
51 LIG N7 na -0.347200 -0.347200 0.748000 1.550000 1.550000
52 LIG C41 cd 0.084000 0.307000 0.018800 1.700000 1.700000
53 LIG C42 c3 0.137100 0.478200 0.131000 1.700000 1.700000
54 LIG C43 cc -0.143000 0.059000 0.459000 1.700000 1.700000
55 LIG H2 ha 0.167000 0.167000 0.167000 1.300000 1.300000
56 LIG H3 ha 0.166000 0.166000 0.166000 1.300000 1.300000
57 LIG H4 ha 0.165000 0.165000 0.165000 1.300000 1.300000
58 LIG H5 ha 0.165000 0.165000 0.165000 1.300000 1.300000
59 LIG H6 ha 0.167000 0.167000 0.167000 1.300000 1.300000
60 LIG H7 ha 0.166000 0.166000 0.166000 1.300000 1.300000
61 LIG H8 ha 0.181000 0.181000 0.181000 1.300000 1.300000
62 LIG H9 ha 0.181000 0.181000 0.181000 1.300000 1.300000
63 LIG H10 ha 0.206000 0.206000 0.206000 1.300000 1.300000
64 LIG H11 h4 0.226000 0.226000 0.226000 1.300000 1.300000
65 LIG H12 h4 0.225000 0.225000 0.225000 1.300000 1.300000
66 LIG H13 h1 0.114700 0.114700 0.114700 1.300000 1.300000
67 LIG H14 h1 0.115700 0.115700 0.115700 1.300000 1.300000
68 LIG H15 h1 0.114700 0.114700 0.114700 1.300000 1.300000
69 LIG H16 ha 0.206000 0.206000 0.206000 1.300000 1.300000
70 LIG H17 ha 0.202000 0.202000 0.202000 1.300000 1.300000
71 LIG H18 h4 0.223000 0.223000 0.223000 1.300000 1.300000
72 LIG H19 h4 0.223000 0.223000 0.223000 1.300000 1.300000
73 LIG H20 h1 0.113700 0.113700 0.113700 1.300000 1.300000
74 LIG H21 h1 0.114700 0.114700 0.114700 1.300000 1.300000
75 LIG H22 h1 0.112700 0.112700 0.112700 1.300000 1.300000
76 LIG H23 ha 0.199000 0.199000 0.199000 1.300000 1.300000
77 LIG H24 ha 0.206000 0.206000 0.206000 1.300000 1.300000
78 LIG H25 h4 0.226000 0.226000 0.226000 1.300000 1.300000
79 LIG H26 h4 0.225000 0.225000 0.225000 1.300000 1.300000
80 LIG H27 h1 0.114700 0.114700 0.114700 1.300000 1.300000
81 LIG H28 h1 0.115700 0.115700 0.115700 1.300000 1.300000
82 LIG H29 h1 0.114700 0.114700 0.114700 1.300000 1.300000
83 LIG H30 ha 0.206000 0.206000 0.206000 1.300000 1.300000
84 LIG H31 ha 0.199000 0.199000 0.199000 1.300000 1.300000
85 LIG H32 h4 0.223000 0.223000 0.223000 1.300000 1.300000
86 LIG H33 h4 0.223000 0.223000 0.223000 1.300000 1.300000
87 LIG H34 h1 0.113700 0.113700 0.113700 1.300000 1.300000
88 LIG H35 h1 0.114700 0.114700 0.114700 1.300000 1.300000
89 LIG H36 h1 0.112700 0.112700 0.112700 1.300000 1.300000
90 LIG H37 ha 0.202000 0.202000 0.202000 1.300000 1.300000
total system charges (+/-) for PB 4.0030 9.4172 -5.4142
cavity_surften = 0.0072 cavity_offset = 0.0000
SAS Surface: surface dots generated: 366
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
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 3535
NB-update: atom-based nb list 2292
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 64.000 43.000 18.000
Xmin, Xmax, Xmax-Xmin: 59.729 68.710 8.981
Ymin, Ymax, Ymax-Ymin: 32.255 53.504 21.249
Zmin, Zmax, Zmax-Zmin: 7.106 28.945 21.839
beginning box center at level 1 64.000 43.000 18.000
beginning box center at level 2 64.000 43.000 18.000
Grid dimension at level 1 5 13 13
Grid origin corrected at level 1 52.000 15.000 -10.000
Grid dimension at level 2 33 57 59
Grid origin corrected at level 2 55.500 28.500 3.000
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000
On Thu, Sep 18, 2014 at 8:12 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, 2014-09-18 at 19:40 +0530, Asfa Ali wrote:
> > Hi,
> >
> > While running mm_pbsa.pl of a ligand-dna complex, I got the following
> error
> > message:
> >
> > /data/software/amber91/exe/pbsa -O -i pbsa.in -o pbsa_lig.77.out -c
> > ./snapshot_lig.crd.77 -p ./lig_vac.prmtop not successful
> >
> > The snapshot_com.all.out and snapshot_rec.all.out are fine, only in the
> > case of lig, it is stopping at 77.
> >
> > I checked the ambermailing list and added the line "fillratio = 4.0" in
> the
> > pbsa.in file generated but still the error persists.
>
> Look for the error message inside pbsa_lig.77.out. Try using that error
> message as a starting point for an online search.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12
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Received on Thu Sep 18 2014 - 11:30:09 PDT
