Thank you very much for your recommendations Carlos. I will take into
account them.
Regards,
Edwin.
On Fri, 2015-03-20 at 17:08 -0400, Carlos Simmerling wrote:
> take a look at our protein folding paper from JACS last year, there are
> lots of methods details. I'd suggest an REMD run since that length can get
> pretty stuck in MD.
> http://pubs.acs.org/doi/abs/10.1021/ja5032776
>
> On Fri, Mar 20, 2015 at 4:47 PM, Edwin Helbert Aponte Angarita <
> helbert2a.gmail.com> wrote:
>
> > Hi, thanks for your replies.
> >
> > I has been shown that this peptide can acquire a conformation in which
> > the two alanine chains form helices, and these two can come close
> > together to form a coiled-coil conformation. We want to simulate this
> > peptide to see if we can get these conformations, measure the collision
> > cross section and compare with travelling wave ion mobility
> > spectrometry. We are hoping that we can sample different conformations
> > at different times from long simulations of this peptide.
> >
> > Regards,
> > Edwin.
> >
> > On Fri, 2015-03-20 at 16:00 -0400, Carlos Simmerling wrote:
> > > this is moving a bit away from the technical error, so if you want better
> > > feedback on what the best choices for your MD might be then it would help
> > > to know a little more about your goals. what do you want to learn about
> > > this peptide?
> > >
> > >
> > > On Fri, Mar 20, 2015 at 3:03 PM, Edwin Helbert Aponte Angarita <
> > > helbert2a.gmail.com> wrote:
> > >
> > > > Hello, thank you for your help.
> > > >
> > > > I will try without counter ions only then, and see if I can get the
> > > > information I want this way.
> > > >
> > > > I will follow the advice from Carlos and use igb=8 with mbondi3, with
> > > > ff14SB.
> > > >
> > > > I am using sander.MPI and I am running in this way:
> > > >
> > > > mpirun -np X sander.MPI -O -i mdin -o mdout -p prmtop -c inpcrd -r rst
> > -x
> > > > mdcrd
> > > >
> > > > where X has been either 8 or 16.
> > > >
> > > > I am new to amber so I haven't tried pmemd, but I will do it soon.
> > > >
> > > > May I be limited to 8 processors also in MD?
> > > >
> > > > I am also simulating the same peptide in TIP3PBOX solvent. So far I
> > haven't
> > > > had problems running it on 16 processors. Could I encounter the same
> > > > problems with this simulation with explicit solvent?
> > > >
> > > > Thanks,
> > > > Edwin.
> > > >
> > > > 2015-03-20 15:26 GMT+00:00 Carlos Simmerling <
> > carlos.simmerling.gmail.com
> > > > >:
> > > >
> > > > > Yes check that, because it's easier to debug a test case failing than
> > > > your
> > > > > specific inputs.
> > > > > Sorry Carlos for the incomplete information.
> > > > >
> > > > > Actually I didn't set any born radii in leap, I didn't know about it
> > but
> > > > > now I do --thanks. So, because I didn't set any born radii, it should
> > > > > have used the default (PBRadii set to mbondi), which according to the
> > > > > manual is the recommended value when using igb=1, which I am using.
> > > > >
> > > > > I don't know about the test because it is run on a cluster but I
> > really
> > > > > think so because the administrators are very careful. I am at the
> > > > > University of Birmingham, UK. I will see if I can get that
> > information.
> > > > >
> > > > > Thanks,
> > > > > Edwin.
> > > > >
> > > > > On Thu, 2015-03-19 at 18:26 -0400, Carlos Simmerling 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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Received on Sat Mar 21 2015 - 05:00:03 PDT
