Here are the inpcrd2, prmtop2 and inpcrd 3 files.
Sanmeet
On Wed, Mar 4, 2015 at 11:44 AM, Sanmeet Chahal <schah063.uottawa.ca> wrote:
> I don't think my first message wen't through so here it is again:
>
> Hello all,
>
> 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.
>
> I am sending three emails to keep the size of the attachments below the
> requirements.
>
> Thanks,
> Sanmeet
>
> On Wed, Mar 4, 2015 at 11:34 AM, Sanmeet Chahal <schah063.uottawa.ca>
> wrote:
>
>> Here is the remaining inpcrd and prmtop files.
>>
>> Best wishes,
>> 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
- application/octet-stream attachment: inpcrd2
- application/octet-stream attachment: prmtop2
- application/octet-stream attachment: inpcrd3
Received on Wed Mar 04 2015 - 09:00:04 PST
