Re: [AMBER] trajectory of minimization using generalized Born

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Fri, 20 Mar 2015 09:25:47 -0400

I can't help with the error right now as I'm traveling, but I would
definitely not recommend using igb=1 for that kind of system. Use igb=8
with mbondi3. Also, if you want counterions in GB you'll need to do careful
testing as we did not do that. Finally, consider ff14SB instead of ff99SB.
On Mar 20, 2015 9:14 AM, "Edwin Helbert Aponte Angarita" <
helbert2a.gmail.com> wrote:

> Thanks Jason,
>
> Using:
> find /gpfs/apps/amber/amber12.0/ -iname \*patch\*
> I didn't find $AMBERHOME/.patches/Amber_Applied_Patches neither
> patch_amber.py. I will ask what patches have been applied. I also did more
> testing and got interesting results.
>
> I want to simulate a peptide, and I am trying to simulate with and without
> counter ion (has net charge of +1). In summary, the system with counter ion
> minimized, but the one without counter ion worked with 8 processors but not
> with 16.I am using these scripts with tleap -f
>
> Without counter ion:
>
> source /gpfs/apps/amber/amber12.0/dat/leap/cmd/leaprc.ff99SB
> AcA14KG3A14K = sequence { ACE ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA
> ALA ALA ALA LYS GLY GLY GLY ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA
> ALA ALA CLYS }
> saveoff AcA14KG3A14K AcA14KG3A14K_linear-ff99SB-noCion.lib
> savepdb AcA14KG3A14K AcA14KG3A14K_linear-ff99SB-noCion.pdb
> saveamberparm AcA14KG3A14K AcA14KG3A14K-ff99SB-noCion.prmtop
> AcA14KG3A14K-ff99SB-noCion.inpcrd
> quit
>
> With counter ion:
>
> source /gpfs/apps/amber/amber12.0/dat/leap/cmd/leaprc.ff99SB
> AcA14KG3A14K = sequence { ACE ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA
> ALA ALA ALA LYS GLY GLY GLY ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA
> ALA ALA CLYS }
> addions AcA14KG3A14K Cl- 0
> saveoff AcA14KG3A14K AcA14KG3A14K_linear-ff99SB-CIon.lib
> savepdb AcA14KG3A14K AcA14KG3A14K_linear-ff99SB-CIon.pdb
> saveamberparm AcA14KG3A14K AcA14KG3A14K-ff99SB-CIon.prmtop
> AcA14KG3A14K-ff99SB-CIon.inpcrd
> quit
>
> And the following mdin file:
>
> &cntrl
> imin=1,
> maxcyc=2000,
> ncyc=1000,
> cut=999.,
> rgbmax=999.,
> igb=1,
> ntb=0,
> ntpr=100,
> ntwx=100,
> ioutfm=1,
> /
>
> I am setting -O -i -o -p -c -r -x properly and these are the results
>
> Without counter ion, 16 processors: failed with ERROR IN SETPAR()
> Without counter ion, 8 processors: succeeded, all minimization steps
> completed
> With counter ion, 16 processors: Succeeded, all minimization steps
> completed
>
> Can you reproduce this error?
>
> Many thanks,
> Edwin.
>
>
>
> 2015-03-20 12:29 GMT+00:00 Jason Swails <jason.swails.gmail.com>:
>
> > 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)
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > 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
> > > > > >
> > > > > _______________________________________________
> > > > > 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
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 20 2015 - 06:30:07 PDT
Custom Search