Daniel,
No I did not get any error messages just the execution time without
any results
On Thu, Nov 5, 2015 at 2:18 PM, Aishani Prem <aishaniprem.gmail.com> wrote:
> Thank You that works!!!
>
> On Thu, Nov 5, 2015 at 2:11 PM, V. Kumar <vin.vasanth.gmail.com> wrote:
>
>> Hi
>>
>> this is another way to obtain rmsd using cpptraj.
>>
>> create a input file "rmsd_cpptraj.trajin"
>> =========================================
>>
>> trajin monA_gb_md1_nocut.mdcrd
>> reference monA_gb_md1_nocut.rst
>> autoimage
>> rms reference mass out monA_gb_md1_nocut_cpptraj.rms time 0.1
>>
>>
>> command
>> $AMBERHOME/bin/cpptraj -p monA_vac.prmtop -i rmsd_cpptraj.trajin >
>> cpptraj.log
>>
>> On 5 November 2015 at 22:45, Aishani Prem <aishaniprem.gmail.com> wrote:
>>
>> > Hello,
>> > I have been working on the amber B1 tutorial. When I use the
>> cpptraj
>> > command to generate the rmsd file I get :-
>> > CPPTRAJ: Trajectory Analysis. V15.00
>> > ___ ___ ___ ___
>> > | \/ | \/ | \/ |
>> > _|_/\_|_/\_|_/\_|_
>> >
>> > | Date/time: 11/05/15 13:29:39
>> > | Available memory: 13178.9 MB
>> >
>> > Reading 'monA_vac.prmtop' as Amber Topology
>> > TIME: Total execution time: 0.0263 seconds.
>> >
>> > But my rmsd is not generated. Can anyone tell me what is the problem.
>> > My input file is :
>> > trajin monA_gb_md1_nocut.mdcrd
>> > rms first mass out monA_gb_md1_nocut.rms time 0.1
>> > and my command is
>> > $AMBERHOME/bin/cpptraj -p monA_vac.prmtop -i monA_gb_md1_nocut.calc_rms
>> > I checked the mdcrd and prmtop files and they seem fine.
>> > --
>> > Thank You and Regards,
>> > Aishani Chittoor Prem
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Thank You and Regards,
> Aishani Chittoor Prem
>
--
Thank You and Regards,
Aishani Chittoor Prem
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Received on Thu Nov 05 2015 - 14:30:06 PST
