Hi,
I'm trying to do analysis on a protein-ligand complex using mmgbsa via
imin=5, igb=1, gbsa=1. my infile is as follows:
##############
&cntrl
imin=5, maxcyc=1, ncyc=1, drms=0.05, ibelly=0,
ntwx=1, ntb=0, cut=50.0, saltcon=0.15,
igb=1, gbsa=1, ntwe=1, ntwr=10000,
&end
##############
I have created a dehydrated inpcrd and topology file without box
information using cpptraj:
*parmstrip :WAT*
*parmstrip :Cl-*
*parmwrite out*
these files open fine in chimera and do not have water or ions. I gave
tested the dehydrated parm with the trajectory that I intend to process as
well and that plays in Chimera too. Issuing the command parmbox gives the
result:
*Box type is 0 (beta=0.000000)*
*
*
However, on running the gbsa simulation, I get the following error. I take
it that messages such as "Unusual nbond for C : 3177" are only
warning regarding the ligand and are not the main issue. Please find
attached my dehydrated topology file, inpcrd and first 10 frames from the
trajectory that is to be processed.
Any help anyone could offer would be much appreciated.
the attached files are:
GS4_Complex_25_NOWAT_nobox.parm: topology file
GS4_Complex_25_NOWAT_nobox.crd: inpcrd
md_out_dehydrated.ncdf: 10 frames of prod md
###########################
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 02/25/2013 at 12:21:27
[-O]verwriting output
File Assignments:
| MDIN: GBSA_energy.in
| MDOUT: GS4_Complex25.out
|INPCRD: ../../../GS4_Complex25_sim/leap/GS4_Complex_25_NOWAT_nobox.crd
| PARM: ../../../GS4_Complex25_sim/leap/GS4_Complex_25_NOWAT_nobox.parm
|RESTRT: GS4_Complex25_GBSA.rst
| REFC: ../../../GS4_Complex25_sim/leap/GS4_Complex_25_NOWAT_nobox.crd
| MDVEL: mdvel
| MDEN: GS4_Complex25_GBSA.mden
| MDCRD: mdcrd
|MDINFO: md_GS4_Complex25_GBSA.mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: ../../../GS4_Complex25_sim/prod/md_out_dehydrated.ncdf
|
Here is the input file:
Min to calculate configurational energies
&cntrl
imin=5, maxcyc=1, ncyc=1, drms=0.05, ibelly=0,
ntwx=1, ntb=0, cut=50.0, saltcon=0.15,
igb=1, gbsa=1, ntwe=1, ntwr=10000,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 02/25/13 Time = 00:23:05
NATOM = 3227 NTYPES = 19 NBONH = 1662 MBONA = 1594
NTHETH = 3795 MTHETA = 2163 NPHIH = 7283 MPHIA = 5032
NHPARM = 0 NPARM = 0 NNB = 17930 NRES = 199
NBONA = 1594 NTHETA = 2163 NPHIA = 5032 NUMBND = 69
NUMANG = 143 NPTRA = 72 NATYP = 48 NPHB = 1
IFBOX = 0 NMXRS = 98 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 232982
| Hollerith 19563
| Integer 319660
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 3145 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 5, 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 =
10000
iwrap = 0, ntwx = 1, ntwv = 0, ntwe =
1
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 1, nsnb =
25
ipol = 0, gbsa = 1, iesp = 0
dielc = 1.00000, cut = 50.00000, intdiel = 1.00000
saltcon = 0.15000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1, ncyc = 1, ntmin = 1
dx0 = 0.01000, drms = 0.05000
| MPI Timing options:
| profile_mpi = 0
Unusual nbond for C : 3177 1
Using default carbon LCPO parameters
Unusual nbond for C : 3185 1
Using default carbon LCPO parameters
Unusual nbond for C : 3202 1
Using default carbon LCPO parameters
Unusual nbond for C : 3206 1
Using default carbon LCPO parameters
Unusual nbond for C : 3224 1
Using default carbon LCPO parameters
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
Cpptraj Generated Restart
begin time read from input coords = 1.000 ps
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 3227
| Running AMBER/MPI version on 1 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
CDF^B^.^.^.
Error in trajectory file
error in trajene()
##############################
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Received on Mon Feb 25 2013 - 05:00:04 PST
