Hello all,
I am still trying to troubleshoot this issue and after testing my procedure
with many different molecules I think that the issue is coming from the
presence of an O-H bond. I followed the same procedure as outlined in the
first post and the segfault only occurs for molecules when they have an O-H
bond even if the rest of the molecule is kept identical.
Here's the link to all of the prmtop and inpcrd files for the runs I did:
https://www.dropbox.com/sh/dd9rjlklkcs9kr1/AAAQ4pKcR8r0mgMzX-hfOS3oa?dl=0
Contents of the link:
*t0s0 = N-methylformamide (no errors - no O-H)
*t0s1 = acetic acid (segfault occcurs - contains O-H)
*t0s2 = propanal (no error - no O-H)
*t0s3 = propanoic acid (segfault occurs - contains O-H)
*t0s4 = methanol (segfault occurs - contains O-H)
*t0s5 = methanal (no error - no O-H)
*t0s6 = methylamine (no error - no O-H)
*t0s7 = diaminomethane (no error - no O-H)
*t0s8 = cyclopentane (no error - no OH)
*t0s9 = benzene (no error - no O-H)
*t0s10 = 4-methylpyridine (no error - no O-H)
*t0s11 = guanidinium (no error - no O-H) I realize that in the first email
I said that the run failed when I tried with guanidinium but that occurred
because the mol2 file used to produce the prmtop and inpcrd files for that
run contained both guanidinium and acetic acid so it was probably the
presence of the acetic acid's O-H that was causing the segfault.
*t0s12 = water (segfault occurs = contains O-H)
In the link you will also find the *.in files I used. I also included the
custom frcmod files and mol2 I use to generate the prmtop and inpcrd files
for *t0s1 and *t0s2.
Let me know if you have any idea of what is causing this error or if you
have made any progress on the issue.
Best wishes,
Sanmeet
On Wed, Mar 4, 2015 at 4:33 PM, Jason Swails <jason.swails.gmail.com> wrote:
> You can stop sending the files.
>
> On Wed, Mar 4, 2015 at 4:32 PM, Sanmeet Chahal <schah063.uottawa.ca>
> wrote:
>
> > Here are the prmtop2, inpcrd2, inpcrd3 files.
> >
> > Sanmeet
> >
> > On Wed, Mar 4, 2015 at 4:29 PM, Sanmeet Chahal <schah063.uottawa.ca>
> > wrote:
> >
> > > Hello all,
> > >
> > > I have been trying to send the following message but I don't think it
> has
> > > reached you as I do not see it present in the AMBER Mailing list
> archive,
> > > please excuse me if this has reached you and you hadn't had the time to
> > > respond.
> > >
> > > I am attaching the prmtop and inpcrd files for all three runs that
> > > succeeded as well as the the case were it failed (the one for acetic
> > acid).
> > >
> > > Legend for the prmtop and inpcrd files attached:
> > > prmtop, inpcrd correspond to the same molecule show in Tutorial B0.
> > > prmtop2, inpcrd2 correspond to the molecule shown in Tutorial B0 but
> the
> > > methyl group removed from the central carbon.
> > > prmtop3, inpcrd3 correspond to the molecule shown in Tutorial B0 with
> > > atoms on half the molecule being removed.
> > > prmtop4, inpcrd4 correspond to acetic acid (that failed).
> > >
> > > I have also attached the input files that I used (they were the same
> for
> > > all the runs) and the 01_Min.out and 01_Min.mdinfo files for the run
> that
> > > failed.
> > >
> > > Also I was using sander from Amber14.
> > >
> > > I am sending three emails to keep the size of the attachments below the
> > > requirements. In this message you will find all the *.in files, the
> first
> > > set of prmtop and inpcrd files and the 01_Min.mdout and 01_Min.out
> files
> > > for the run that failed.
> > >
> > > Thanks,
> > > Sanmeet
> > >
> > > On Wed, Mar 4, 2015 at 8:10 AM, David A Case <case.biomaps.rutgers.edu
> >
> > > wrote:
> > >
> > >> On Tue, Mar 03, 2015, Sanmeet Chahal wrote:
> > >> >
> > >> > I am a new Amber user and so I followed and completed Tutorial B0 up
> > to
> > >> the
> > >> > point of VMD visualization of the result.
> > >> >
> > >> > I am now trying to repeat the tutorial up to this point with a
> prmtop
> > >> and
> > >> > inpcrd files that I produce using tleap and a customized frcmod
> file.
> > >> Here
> > >> > are the steps I take:
> > >>
> > >> >
> > >> > I have attached images of the molecules with which I was able to
> > >> complete
> > >> > the tutorial using prmtop and inpcrd files produced with steps 1-6.
> > >>
> > >> We will need to get the actual prmtop and inpcrd files to try to debug
> > >> a segfault problem. Was there any output in the mdout file from the
> > >> minimzation step that failed?
> > >>
> > >> ...thanks...dac
> > >>
> > >>
> > >> _______________________________________________
> > >> 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
>
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Received on Fri Mar 06 2015 - 13:30:02 PST
