AMBER Archive (2009)

Subject: Re: [AMBER] please help me out

From: bharat lakhani (lakhbharat_at_gmail.com)
Date: Mon Mar 23 2009 - 02:58:52 CDT

respected sir,
                      Here i am sending a file,It includes a protein
molecule and ligand molecule.My ligand molecule has a sulphur group.but whem
i am minimizing this structure with sander.It remove that sulphur from the
ligand and making it as a point outside the lingand seprately.And after this
i am getting binding affinity -5.24 Kcal/mol.But i am expecting much
better.Is any body please help me out,I apprecitae that

On Sat, Mar 14, 2009 at 10:24 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Bharat,
>
> Chances are that your initial structure is bad and this is causing some
> division by zero somewhere that is giving an infinite energy and causing
> the
> code to crash. Unfortunately when running in parallel such problems can be
> hard to detect and error messages can get lost in places and output not
> generated. This occurs because only one of the threads likely crashed and
> the others are waiting at a barrier somewhere and so the code appears to
> hang. In such cases it is advisable to try things out in serial and see
> what
> happens. At least here you will be able to see any error messages etc.
>
> I would also just try running the first 100 steps or so of minimization and
> set ntpr=1. In that way you will be able to see if any problems exist with
> the initial structure and possibly track them down.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > Behalf Of bharat lakhani
> > Sent: Saturday, March 14, 2009 4:05 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] please help me out
> >
> > Respected sir,
> > When i am running sander for my complex
> > minimization.It is generating following output.
> >
> >
> > -------------------------------------------------------
> > Amber 9 SANDER 2006
> > -------------------------------------------------------
> >
> > | Run on 03/07/2009 at 06:02:48
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: minvac.in
> >
> > | MDOUT:
> > DRUG0minvac.out
> > |INPCRD:
> > DRUG0.crd
> > | PARM:
> > DRUG0.top
> > |RESTRT:
> > DRUG0minvac.crd
> > | REFC:
> > refc
> > | MDVEL:
> > mdvel
> > | MDEN:
> > mden
> > | MDCRD:
> > mdcrd
> > |MDINFO:
> > mdinfo
> > |INPDIP:
> > inpdip
> > |RSTDIP:
> > rstdip
> >
> >
> > Here is the input file:
> >
> > in vacuo
> > minimization
> > &cntrl
> >
> > imin =
> > 1,
> > maxcyc =
> > 1000,
> > ncyc =
> > 200,
> > ntb =
> > 0,
> > igb =
> > 0,
> > cut =
> > 12
> > /
> >
> >
> >
> --------------------------------------------------------------------------
> > ------
> > 1. RESOURCE USE:
> >
> --------------------------------------------------------------------------
> > ------
> >
> > | Flags:
> > MPI
> > | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> > |Largest sphere to fit in unit cell has radius = 49.070
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 03/07/09 Time = 06:02:30
> > NATOM = 2506 NTYPES = 15 NBONH = 1241 MBONA = 1297
> > NTHETH = 2798 MTHETA = 1764 NPHIH = 5299 MPHIA = 3375
> > NHPARM = 0 NPARM = 0 NNB = 13749 NRES = 160
> > NBONA = 1297 NTHETA = 1764 NPHIA = 3375 NUMBND = 52
> > NUMANG = 108 NPTRA = 43 NATYP = 38 NPHB = 0
> > IFBOX = 0 NMXRS = 39 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> >
> > | Memory Use Allocated
> > | Real 160042
> > | Hollerith 15198
> > | Integer 249443
> > | Max Pairs 1443456
> > | nblistReal 30072
> > | nblist Int 1046806
> > | Total 12246 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 = 0, nsnb =
> > 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
> > scnb = 2.00000, scee = 1.20000
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Energy minimization:
> > maxcyc = 1000, ncyc = 200, ntmin = 1
> > dx0 = 0.01000, drms = 0.00010
> > | INFO: Old style inpcrd file read
> >
> >
> >
> --------------------------------------------------------------------------
> > ------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> --------------------------------------------------------------------------
> > ------
> >
> >
> >
> > begin time read from input coords = 0.000 ps
> >
> > Number of triangulated 3-point waters found: 0
> > | Atom division among processors:
> > | 0 322 632 948 1270 1570 1879 2201
> > | 2506
> >
> > Sum of charges from parm topology file = -1.00003006
> > | Running AMBER/MPI version on 8 nodes
> >
> >
> >
> --------------------------------------------------------------------------
> > ------
> > 4. RESULTS
> >
> --------------------------------------------------------------------------
> > ------
> >
> > ---------------------------------------------------
> >
> > eedmeth=4: Setting switch to one everywhere
> >
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST = 66786
> > | TOTAL SIZE OF NONBOND LIST = 524450
> >
> > Why it is not minimizing my complex.i do not know.my be the cavity size
> of
> > my complex is not as much as it has to be.please help me out
>
>
>
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