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 - 13:30:03 PDT
