Hello all,
Sorry to bring up an old issue, but I was reading the amber14 manual and on
page 245 found the following example:
# Make atoms 40, 41, 42, and 57 a new LJ type with 0s for
# their parameters to remove all of their LJ interactions
# with every other atom
addLJType .40-42,57 0.0 0.0
I'm confused because it seems that having the epsilon as 0.0 was what was
causing the segfault when I ran the run minimization step of Tutorial B0
because after changing the epsilon to be a non-zero value the error stopped
occurring. Could some one please explain when it is ok to set LJ parameters
to 0 and when they could cause an error?
I have experimented with setting different values of epsilon and found that
no error occurred when epsilon is 1E-25 but the segfault occurs when
epsilon is 1E-30.
Thank-you,
Sanmeet
On Fri, Mar 6, 2015 at 7:06 PM, Sanmeet Chahal <schah063.uottawa.ca> wrote:
> 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 Mon Mar 09 2015 - 14:30:03 PDT
