Dear Jason,
I used xleap to create these prmtop and inpcrd files for the NDM molecule.
Because my ndm molecule contains 3 Zinc atoms which are not defined atom
types in AMBER, I created them as non-standard residues using the tutorial
A1 (advanced version) from Dr. Walker.
I followed the steps in the tutorial. The new atom types are HIZ (His56),
HIA (His95), HIO (His125), CYM (Cys144), and CL (clorua ion) lib. The
charges for these atoms were Mulliken charges taken from Gaussian running.
And all the Zn parameters are from Ryde 1995 and Dr. Walker's thesis.
For the second points you said about the number of water atoms added, I
actually tried with both TIP3PBOX 8.0 and TIP3PBOX 12, but got the same
errors.
Please take a look and help me.
Thank you.
Chinsu
On Thu, May 19, 2011 at 11:30 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Chinsu,
>
> I received your topology file and looked at it, and I know why you're
> getting the error that you're getting. My question is where and how
> *exactly* did you create your topology file? If you tried to hack the
> topology file yourself to add stuff, then you need to be more wary of what
> you change, and be willing to track down problems like these. If you used
> some program or script to build your topology file, then there is a bug
> with
> that program or script (I haven't been able to reproduce this error with
> simple leap scripts in either sleap or tleap). If you can provide the
> exact
> method you used to create this topology file it may help other people avoid
> similar fates.
>
> The problem is that not every atom is assigned to a molecule. That is, if
> you add up every number in the prmtop section ATOMS_PER_MOLECULE, it comes
> out to 24550, yet NATOM in that prmtop is defined as 24559. Thus, the last
> 9 atoms (last 3 water molecules) are not assigned to any molecules. This
> will cause a segfault for a large number of compilers (if you're lucky --
> otherwise it just spits out bogus results). The actual problem is that the
> first "molecule" is actually 2293 atoms large, yet ATOMS_PER_MOLECULE lists
> it as 2284. If you make this change, it *should* work, but since I don't
> know how this prmtop was created and I already know there's one problem
> with
> it, I wouldn't trust it at all. Note that ONLY constant pressure
> simulations use molecule information (to do pressure scaling), so this
> segfault will only occur when you try NTP simulations.
>
> HTH,
> Jason
>
> On Wed, May 18, 2011 at 10:31 PM, Chinh Su Tran To <
> chinh.sutranto.gmail.com
> > wrote:
>
> > Dear Jason,
> >
> > The files are too big. Please dont mind if i sent them to your email.
> > Thank you.
> >
> > Chinsu
> >
> > On Thu, May 19, 2011 at 2:14 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > Can you attach your input files? This includes the topology file,
> > inpcrd,
> > > and mdin. Segfaults are indicative of memory errors, but it's not at
> all
> > > specific.
> > >
> > > There may be something subtly wrong with your topology file, or it may
> be
> > a
> > > bug.
> > >
> > > All the best,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > >
> > > On May 18, 2011, at 1:00 AM, Chinh Su Tran To <
> chinh.sutranto.gmail.com>
> > > wrote:
> > >
> > > > Dear Amber users,
> > > >
> > > > Again i got the same error of "segmentation fault" even whatever i
> > > modified
> > > > my batch-file. The "ndm_md1.rst" was not even created.
> > > >
> > > > I compared the "ndm_md1.out" with other successful runs (i.e other
> > > > "xx_md1.out"), i found that the process of running wat-md1.in was
> > halted
> > > in
> > > > the first step, as shown below (this is extracted from the
> > > "ndm_md1.out"):
> > > >
> > > > *NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> =
> > > > 0.0
> > > > Etot = -64769.2683 EKtot = 0.0000 EPtot =
> > > > -64769.2683
> > > > BOND = 79.7941 ANGLE = 500.8945 DIHED =
> > > > 1498.9190
> > > > 1-4 NB = 453.3799 1-4 EEL = 7256.7348 VDWAALS =
> > > > 10279.1689
> > > > EELEC = -84838.1594 EHBOND = 0.0000 RESTRAINT =
> > > > 0.0000
> > > > Ewald error estimate: 0.8471E-04
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > > *
> > > >
> > > > Please help. I really have no idea what is going on. I think the
> > > > "ndm_md1.rst" had not been created because the process stopped
> > > unexpectedly.
> > > >
> > > > Thank you.
> > > > Chinsu
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, May 16, 2011 at 7:46 PM, Chinh Su Tran To
> > > > <chinh.sutranto.gmail.com>wrote:
> > > >
> > > >> Dear Jason,
> > > >>
> > > >> This is my batch file:
> > > >>
> > > >> */usr/local/amber10/exe/sander -O -i ./file-in/wat-min1.in -o
> > > >> ./results/ndm_min1.out -p ./results/ndm-wat.prmtop -c
> > > >> ./results/ndm-wat.inpcrd -r ./results/ndm_min1.rst -ref
> > > >> ./results/ndm-wat.inpcrd
> > > >>
> > > >> /usr/local/amber10/exe/sander -O -i ./file-in/wat-min2.in -o
> > > >> ./results/ndm_min2.out -p ./results/ndm-wat.prmtop -c
> > > ./results/ndm_min1.rst
> > > >> -r ./results/ndm_min2.rst
> > > >>
> > > >>
> > > >> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md1.in -o
> > > >> ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> > > ./results/ndm_min2.rst
> > > >> -r ./results/ndm_md1.rst -x ./results/ndm_md1.mdcrd -ref
> > > >> ./results/ndm_min2.rst
> > > >>
> > > >> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md2.in -o
> > > >> ./results/ndm_md2.out -p ./results/ndm-wat.prmtop -c
> > > ./results/ndm_md1.rst
> > > >> -r ./results/ndm_md2.rst -x ./results/ndm_md2.mdcrd
> > > >>
> > > >> /usr/local/amber10/exe/ambpdb -p ./results/ndm-wat.prmtop <
> > > >> ./results/ndm_md2.rst > ./results/ndm_md2.pdb*
> > > >>
> > > >> And the part below is the error I got:
> > > >>
> > > >>
> > > >> **/var/spool/torque/mom_priv/*
> > > >> *jobs/5731.bircibm.SC <http://5731.bircibm.sc/>: line 17: 14885
> > > >>> Segmentation fault /usr/local/amber10/exe/sander -O -i
> > ./file-in/
> > > >>> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> > > >>> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
> > > >> ./results/ndm_md1.mdcrd
> > > >>> -ref ./results/ndm_min2.rst
> > > >>>
> > > >>> Unit 30 Error on OPEN:
> > > >>> ./results/ndm_md1.rst
> > > >>> /var/spool/torque/mom_priv/**jobs/5731.bircibm.SC<
> > > http://5731.bircibm.sc/>:
> > > >> line 25:
> > > >>> ./results/ndm_md2.rst: No such file or directory
> > > >>
> > > >> *
> > > >> I double-checked and found that the ndm_md1.rst was not created,
> > causing
> > > >> the next command was not performed, so the second error led to
> "could
> > > not
> > > >> open the ndm_md2.rst"
> > > >>
> > > >> I viewed other threads from Amber archive titled "segmentation
> fault"
> > > >> saying about "molecular size", but i dont think this error was
> > addressed
> > > >> because i ran the similar batch file for other larger molecules and
> > they
> > > ran
> > > >> fine.
> > > >>
> > > >> Is it possible that it was related to the TIP3PBOX of solvent I
> used?
> > I
> > > >> used TIP3PBOX 12 for this molecule.
> > > >>
> > > >> Thanks for your reply, and hope more help.
> > > >>
> > > >> Chinsu
> > > >>
> > > >>
> > > >> On Mon, May 16, 2011 at 7:27 PM, Jason Swails <
> jason.swails.gmail.com
> > > >wrote:
> > > >>
> > > >>> On Mon, May 16, 2011 at 6:42 AM, Chinh Su Tran To
> > > >>> <chinh.sutranto.gmail.com>wrote:
> > > >>>
> > > >>>> Dear Amber users,
> > > >>>>
> > > >>>> Below is the error I encountered when running a batch file of
> sander
> > > for
> > > >>> MD
> > > >>>> runs following 2-step minimization:
> > > >>>>
> > > >>>> */var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 17: 14885
> > > >>>> Segmentation fault /usr/local/amber10/exe/sander -O -i
> > ./file-in/
> > > >>>> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop
> -c
> > > >>>> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
> > > >>> ./results/ndm_md1.mdcrd
> > > >>>> -ref ./results/ndm_min2.rst
> > > >>>>
> > > >>>> Unit 30 Error on OPEN:
> > > >>>> ./results/ndm_md1.rst
> > > >>>> /var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 25:
> > > >>>> ./results/ndm_md2.rst: No such file or directory
> > > >>>> *
> > > >>>>
> > > >>>
> > > >>> I don't think you copied everything over correctly. Here it says
> > that
> > > >>> ./results/ndm_md2.rst doesn't exist, but I don't see anywhere above
> > > where
> > > >>> you used that file.
> > > >>>
> > > >>>
> > > >>>> could anyone please give me a hint about this? I just dont
> > understand
> > > >>> why
> > > >>>> it
> > > >>>> happened 'cause it ran fine for other molecules before. And why
> > didnt
> > > it
> > > >>>> occur during minimization?
> > > >>>>
> > > >>>> Thank you very much, and really looking forward to your reply.
> > > >>>>
> > > >>>> Regards,
> > > >>>> Chinsu
> > > >>>>
> > > >>>> _______________________________________________
> > > >>>> AMBER mailing list
> > > >>>> AMBER.ambermd.org
> > > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>
> > > >>>>
> > > >>>
> > > >>>
> > > >>> --
> > > >>> Jason M. Swails
> > > >>> Quantum Theory Project,
> > > >>> University of Florida
> > > >>> Ph.D. Candidate
> > > >>> 352-392-4032
> > > >>> _______________________________________________
> > > >>> 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
> > >
> > > _______________________________________________
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> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 18 2011 - 21:30:03 PDT
