Re: [AMBER] trajectory of minimization using generalized Born

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 20 Mar 2015 08:29:03 -0400

The output file printed in an earlier email confirms mbondi:

Implicit solvent radii are modified Bondi radii
(mbondi)

‚ÄčAlso, check $AMBERHOME/.patches/Amber_Applied_Patches

Are there any files in there? If not, you will have to ask the cluster
administrator what patches have been applied. There's nothing we can do if
someone discards all of that information :).

Also -- is there a patch_amber.py script? If so, then the Amber
installation is *very* out-of-date, and I would recommend that you request
an update.

All the best,
Jason‚Äč

On Thu, Mar 19, 2015 at 6:26 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> Thanks, but I also asked which radii set you used in leap. Also, did it
> pass the tests? Until we know those we can't help.
> On Mar 19, 2015 6:05 PM, "Edwin Helbert Aponte Angarita" <
> helbert2a.gmail.com> wrote:
>
> > I am using the The Hawkins, Cramer, Truhlar model (igb=1). I am using
> > rgbmax=999. and cut=999.
> >
> > Thanks,
> > Edwin.
> >
> > On Thu, 2015-03-19 at 16:35 -0400, Carlos Simmerling wrote:
> > > 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)
> > > > >
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> > > >
> > > >
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-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 20 2015 - 05:30:08 PDT
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