On Mon, Jun 26, 2017 at 9:30 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> Thank you, sir, for your kind reply. Is it possible to install amber 14 with amber tools 17 ???
Yes indeed. They will install into separate directories. You can use
pmemd from amber 14 (it does not rely on AMBERHOME being set) and
everything else from AmberTools 17.
-Dan
>
> Thanks and regards,
> Saikat
>
>
> On Monday, 26 June 2017 6:21 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>
> Hi,
>
> There was a minor bug in cpptraj that was fixed very recently having
> to do with TRR files. I recommend upgrading to cpptraj from AmberTools
> 17 (http://ambermd.org/AmberTools17-get.html) or downloading from
> GitHub (https://github.com/Amber-MD/cpptraj) and try your conversion
> again. In fact, cpptraj now supports writing to directly to XTC so you
> could try that as well.
>
> Hope this helps,
>
> -Dan
>
> On Mon, Jun 26, 2017 at 1:06 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
>> Thank you, sir, for your kind response I am using AMBER14 .
>>
>>
>> On Saturday, 24 June 2017 5:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>
>> What version of cpptraj are you using?
>>
>> -Dan
>>
>> On Sat, Jun 24, 2017 at 7:55 AM Saikat Pal <saikatpaliitg.yahoo.com> wrote:
>>
>>> Dear all,
>>> Using cpptraj I have converted .mdcrd to .trr gromacs trajectory .But for
>>> conversion .trr to .xtc file gromacs shows error. I have used this command :
>>> trjconv -s output1.pdb -f gromacs.trr -o md_0_1.xtc -pbc whole -ur compact
>>> it shows this error:WARNING no output, last frame read at t=0
>>> IS that amber amber or gromacs problem ??
>>>
>>> Thanks and regards,
>>>
>>> Saikat
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> 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
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jul 05 2017 - 06:00:06 PDT
