No worries. Found out what the issue was. Our installation of amber was not
configured for netcdf trajectories (which i had decided to use in the
interests of saving space). hence the error. just posting in case anyone
else has the same issue.
On 25 February 2013 12:42, ET <sketchfoot.gmail.com> wrote:
> 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 - 15:00:04 PST
