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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> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
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> > > > > > > >
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> > > > > >
> > > > > > _______________________________________________
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Received on Fri Mar 20 2015 - 14:30:03 PDT
