Just to follow up, not sure which command you were using, but
'multidihedral' does allow you to create and use custom dihedral
definitions, e.g.
multidihedral aibphi:C:N1:C1:C6:-1
(Perhaps this is what you already did?)
-Dan
On Mon, May 8, 2017 at 1:37 PM, Chetna Tyagi <cheta231.gmail.com> wrote:
> Thanks so much Elvis..this worked for me..
>
> On Mon, May 8, 2017 at 6:51 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
>> It will be easier to change atom masks while using cpptraj than change
>> atoms names in trajectories.
>>
>> Best Regards
>>
>>
>>
>> Elvis Martis
>> Ph.D. Student (Computational Chemistry)
>> at Bombay College of Pharmacy
>>
>>
>> A Kalina, Santacruz [E], Mumbai 400098, INDIA
>> W www.elvismartis.in
>> Skype. adrian_elvis12
>>
>>
>>
>>
>> -----Original Message-----
>> From: Chetna Tyagi [mailto:cheta231.gmail.com]
>> Sent: Monday, May 08, 2017 8:38 PM
>> To: amber.ambermd.org
>> Subject: [AMBER] Cpptraj calculates only three PHI-PSI angles in a
>> 18-residue long peptide
>>
>> Dear all,
>>
>> I have a peptide with few non-standard amino acid residues which I made
>> using RED server and carried out this 100 ns long simulation. All other
>> analysis like time-evolution of Hydrogen bonds and RMSD is calculated
>> without errors. But while calculating phi-psi angles as a function of time
>> it only calculates for three residues each. These 3 residues are the
>> standard ones.
>>
>> Phi-4, Phi-5, Phi-15 and Psi-3, Psi-4, Psi-14
>>
>> The error for other angle calculation is "one or more atom masks have no
>> atoms"
>>
>> I believe it can be due to a different atom numbering convention being
>> used, like CA is C1 and C is C6 or C7 etc. The same happens when I compute
>> these angles using the Python MDtraj online module. How can I change this
>> in a trajectory? Is it possible?
>>
>> Thanks in advance
>>
>> --
>> Best wishes
>> Chetna
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Best wishes
> Chetna
> _______________________________________________
> 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 Mon May 08 2017 - 13:30:03 PDT
