Hello all,
I have solved the issue. I was setting the epsilon (in the NONB section of
the frcmod file) for the H in the O-H bond to 0 which was causing the
error.
Best wishes,
Sanmeet
On Fri, Mar 6, 2015 at 4:25 PM, Sanmeet Chahal <schah063.uottawa.ca> wrote:
> 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 - 16:30:02 PST
