Hi Dan,
Thanks for your answer. I forgot to mentioned that I have done "autoimge"
on the entire trajectory and that horrible structure appeared suddenly.
But I have few problems again:
as you suggest to do re-imging the restart file using "autoimage", but I
can not figure out how to do that. I read the manual and planned to do
using
trajin prodrun47.rst
autoimage
trajout imagedprodrun47.rst
*Problem1*: Does that restart file retain the time and velocity
information?
I found that the writing format is different in the newly generate restart
file and is not recognized by pmemd.
Should I use "remdtraj" option? but I am unable to figure out the correct
syntax?
*Problem2: *If this problem solved by re-imaging the restart file, do I
need to redo the entire simulation from beginning by re-imaging each
restart file or I can finish the last few runs of this simulation by doing
re-imaging?
*Problem3:*Two other MD simulations of this system in mutated form were
done. They do not show such anomaly. Do I need to do the same re-imaging
for them also?
Looking forward for your reply.
regards
Aditya
On Fri, Dec 12, 2014 at 8:25 PM, Indrajit Deb <biky2004indra.gmail.com>
wrote:
>
>
>
>
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
>
> ---------- Forwarded message ----------
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Date: Fri, Dec 12, 2014 at 8:20 PM
> Subject: Re: [AMBER] Problem with simulation of protein-DNA complex
> To: AMBER Mailing List <amber.ambermd.org>
>
> Hi,
>
> Have you looked at your entire trajectory? This sounds like it could
> be an imaging artifact to me. Because the DNA is two separate
> molecules, occasionally one strand gets imaged and the other doesn't.
> This has no affect during the simulation since it's just for
> visualization, but it is particularly bad if you have restraints that
> depend on the DNA molecules because restraints are *not* imaged.
> Whenever I simulate multiple solute molecules with PBC and restraints
> I always re-image my coordinate files before restarting. You should
> try re-imaging your restart with cpptraj's 'autoimage' command (the
> one you used as coordinates for the run that blew up) and see if that
> helps.
>
> If on the other hand you've viewed your trajectory and the DNA is
> actually falling apart gradually (i.e. there is no sudden "jump" from
> imaging) that's another story.
>
> -Dan
>
> On Fri, Dec 12, 2014 at 1:49 AM, Aditya Sarkar <aditya.molbio.gmail.com>
> wrote:
> > Dear Amber users,
> >
> > I am new to the MD simulation. I have faced a strange problem in doing
> > simulation of protein-DNA complex. The problem, questions and the setup
> > details are given below:
> >
> > *****PROBLEM********
> > ---------------------------------
> >
> > I have planned to run 100ns simulation and divide the whole run in 50
> > restart (each of 2ns). My simulation ran well upto 94ns but at the
> begining
> > of the next restart I found the DNA get horribly denatured. I have
> attached
> > the picture with this mail.
> >
> > *****QUESTION********
> > ---------------------------------
> >
> > 1. I have checked the prmtop file with rdparm to make sure about the use
> of
> > proper force field. But I have doubt whether my way of selection of force
> > field is correct or not? and also regarding the production run script.
> >
> > 2. I did not get why the DNA get unstable and how can I analyze the cause
> > and correct it?
> >
> >
> > *****SETUP********
> > ---------------------------
> >
> > 1. The structure is a crystal structure with all crystal water. DNA
> residue
> > no: 103-138
> >
> > *2.Force field used: ff99SB-ILDN along with parambsc0*
> >
> > *[tleap file command: source leaprc.ff99SBildn*
> > * loadoff DNA_CI.lib*
> > * loadamberparams frcmod.parmbsc0*
> >
> >
> > *I do did energy minimization (with and without position restraint,
> heating
> > (with position restraint), NPT equilibration (gradually relaxing
> restraint)
> > and finally performed production run*
> >
> > *3.Production run:*
> > &cntrl
> > imin = 0, irest = 1, ntx = 5,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 8.0, ntr = 0,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, gamma_ln = 1.0, ig = -1, iwrap = 1,
> > nstlim = 1000000, dt = 0.002, nmropt =1,
> > ntpr = 2500, ntwx = 2500, ntwr = 2500,
> > ntwv = 2500, ntwe = 2500
> > /
> > &wt type='DUMPFREQ', istep1=2000
> > /
> > &wt type='END'
> > /
> > LISTOUT=POUT
> > DISANG=DIST.rst
> > DUMPAVE=rest_values_INPRORUN1
> > END
> >
> > *4. Distance restraint input file*
> > 2 ALA O 6 ALA N 3.0
> > 3 LEU O 7 ARG N 3.0
> > 53 ALA O 57 ALA N 3.0
> > 54 LEU O 58 ARG N 3.0
> > 50 LEU N 46 ARG O 2.9
> > 49 LYS N 45 ALA O 3.2
> > 101 LEU N 97 ARG O 3.0
> > 100 LYS N 96 ALA O 3.0
> > 103 DG5 O6 138 DC3 H41 2.0
> > 103 DG5 H1 138 DC3 N3 1.9
> > 103 DG5 H22 138 DC3 O2 3.5
> > 121 DG5 O6 120 DC3 H41 1.9
> > 121 DG5 H1 120 DC3 N3 1.9
> > 121 DG5 H22 120 DC3 O2 3.5
> >
> > *5. Commands used:*
> >
> > to generate DIST.rst file:
> > ****************************
> > makeDIST_RST -upb DNA_Protein-endDISTRST -pdb emin_NoRST.pdb -rst
> DIST.rst
> >
> >
> > For production run:
> > **********************
> > nohup mpiexec.hydra -n 8 sander.MPI -O -i production1.in -o
> prodrun1.out -p
> > GCN4_CREB_inbox.prmtop -c equil_NPT.rst -r prodrun1.rst -x prodrun1.mdcrd
> >
> > nohup mpiexec.hydra -n 8 pmemd.MPI -O -i production2.in -o prodrun2.out
> -p
> > GCN4_CREB_inbox.prmtop -c prodrun1.rst -r prodrun2.rst -x prodrun2.mdcrd
> >
> > *NOTE: I was initially unsure about using "pmemd" that's why I started
> > first run with sander and after reading maual and Amber blog, I started
> > using "pmemd".
> >
> >
> > Looking forward for your reply.
> >
> > regards
> > Aditya
> >
> > _______________________________________________
> > 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
>
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Received on Fri Dec 12 2014 - 22:30:02 PST
