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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 19 2015 - 13:00:03 PDT
