And here are the prmtop3, inpcrd4, and prmtop4 and 01_Min.out files. Sorry
for sending multiple messages.
Sanmeet
On Wed, Mar 4, 2015 at 11:47 AM, Sanmeet Chahal <schah063.uottawa.ca> wrote:
> 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
>>>>
>>>
>>>
>>
>
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- application/octet-stream attachment: prmtop3
- application/octet-stream attachment: inpcrd4
- application/octet-stream attachment: prmtop4
Received on Wed Mar 04 2015 - 09:00:04 PST
