did your installation pass the test cases?
also, the GB model and radii set may be more relevant than the force field,
which are you using?
On Thu, Mar 19, 2015 at 4:21 PM, Edwin Helbert Aponte Angarita <
helbert2a.gmail.com> wrote:
> Hi, I think it is worth pointing out that I am using ff99SB.
>
> Thanks.
>
> On Thu, 2015-03-19 at 19:30 +0000, Edwin Helbert Aponte Angarita wrote:
> > Hello, thank you for your replies.
> >
> >
> > I am using Amber 12.0 on a cluster running Scientific Linux 6.6
> > (kernel 2.6.32-504.3.3) and manages jobs using torque.
> >
> >
> > I got the following message when loading amber:
> >
> > module load apps/amber/v12.0
> > Amber and AmberTools v12.0 serial and parallel
> > OpenMPI v1.6.3 for Intel 2013.0.079 with torque and infiniband support
> > Intel compilers v2013.0.079
> >
> >
> > I haven't found update_amber anywhere, maybe the administrator deleted
> > it. I looked for it using:
> > find /gpfs/apps/amber/amber12.0/ -iname \*update\*
> >
> >
> > Is there any other way I can check the patches applied?
> >
> >
> > I am getting an ERROR IN SETPAR() in the .out file:
> >
> > &cntrl
> >
> > imin=1,
> >
> > maxcyc=2000,
> >
> > ncyc=1000,
> >
> > cut=999.,
> >
> > rgbmax=999.,
> >
> > igb=1,
> >
> > ntb=0,
> >
> > ntpr=50,
> >
> > ntwx=50,
> >
> > ioutfm=1,
> > /
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> --------------------------------------------------------------------------------
> >
> > | Flags:
> > MPI
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 03/17/15 Time = 17:22:13
> > NATOM = 352 NTYPES = 8 NBONH = 178 MBONA = 173
> > NTHETH = 397 MTHETA = 236 NPHIH = 718 MPHIA = 679
> > NHPARM = 0 NPARM = 0 NNB = 1863 NRES = 34
> > NBONA = 173 NTHETA = 236 NPHIA = 679 NUMBND = 12
> > NUMANG = 25 NPTRA = 24 NATYP = 10 NPHB = 0
> > IFBOX = 0 NMXRS = 23 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> > Implicit solvent radii are modified Bondi radii
> > (mbondi)
> >
> > | Memory Use Allocated
> > | Real 25582
> > | Hollerith 1092
> > | Integer 38655
> > | Max Pairs 1
> > | nblistReal 0
> > | nblist Int 0
> > | Total 355 kbytes
> >
> > | Note: 1-4 EEL scale factors were NOT found in the topology file.
> > | Using default value of 1.2.
> >
> > | Note: 1-4 VDW scale factors were NOT found in the topology file.
> > | Using default value of 2.0.
> > | Duplicated 0 dihedrals
> > | Duplicated 0 dihedrals
> >
> >
> --------------------------------------------------------------------------------
> > 2. CONTROL DATA FOR THE RUN
> >
> --------------------------------------------------------------------------------
> >
> > ACE
> >
> > 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 = 50, ntwv = 0, ntwe
> > = 0
> > ioutfm = 1, ntwprt = 0, idecomp = 0,
> > rbornstat= 0
> >
> > Potential function:
> > ntf = 1, ntb = 0, igb = 1, nsnb
> > = 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
> > saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
> > gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
> > rdt = 0.00000, rgbmax = 999.00000 extdiel = 78.50000
> > alpb = 0
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Energy minimization:
> > maxcyc = 2000, ncyc = 1000, ntmin = 1
> > dx0 = 0.01000, drms = 0.00010
> >
> > | MPI Timing options:
> > | profile_mpi = 0
> > | INFO: Old style inpcrd file read
> >
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> --------------------------------------------------------------------------------
> >
> > ACE
> > begin time read from input coords = 0.000 ps
> >
> > Number of triangulated 3-point waters found: 0
> > ERROR IN SETPAR() upon atom distribution
> >
> > -------------------------------------------------
> >
> >
> > However, if I run the same minimize the same system with the
> > following .in file everything works:
> >
> >
> >
> > &cntrl
> >
> > imin=1,
> >
> > maxcyc=200,
> >
> > ncyc=100,
> >
> > cut=999.,
> >
> > rgbmax=999.,
> >
> > igb=1,
> >
> > ntb=0,
> >
> > ntpr=5,
> >
> > ntwx=5,
> >
> > ioutfm=1,
> > /
> >
> >
> > Thanks,
> >
> >
> > Edwin.
> >
> >
> >
> >
> >
> >
> > 2015-03-19 2:50 GMT+00:00 Daniel Roe <daniel.r.roe.gmail.com>:
> > Hi,
> >
> > On Wed, Mar 18, 2015 at 10:41 AM, Edwin Helbert Aponte
> > Angarita
> > <helbert2a.gmail.com> wrote:
> > > and I get a very nice plot showing how the peptide converges
> > to a local
> > > minimum and does not change noticeable any more. However, I
> > cannot get
> > > sander nor sander.MPI to write the trajectory file if I use
> > generalized
> > > Born implicit solvent. In that case I use:
> >
> > Do you get any output at all (i.e. in your mdout or mdinfo
> > files)? Are
> > your GB simulations completing without error?
> >
> > -Dan
> >
> > >
> > > &cntrl
> > > imin=1,
> > > maxcyc=2000,
> > > ncyc=1000,
> > > cut=999.,
> > > rgbmax=999.,
> > > igb=1,
> > > ntb=0,
> > > ntpr=50,
> > > ntwx=50,
> > > ioutfm=1,
> > > /
> > >
> > > and I am setting approppriatelly -i -o -p -c -r -x.
> > >
> > > Do you know how can I get the trajectory when using
> > generalized Born
> > > implicit solvent? I only found a very old similar post (
> > > http://archive.ambermd.org/200502/0076.html) but is not
> > really helpful.
> > >
> > > Thanks,
> > >
> > > Edwin.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
>
>
>
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Received on Thu Mar 19 2015 - 14:00:02 PDT
