Ptraj does not accept spaces in mask expressions; try :24.N,CA,C instead.
On Tue, Jun 7, 2011 at 7:04 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Thanks Thomas,
>
> I tried for a particular residue (number 24) as you had suggested,
>
> rms reference out rmsd_bb.dat : 24 .N,CA,C
> rms reference out rmsd_sc.dat : 24 .N,CA,C,O,H
>
>
> The two sets of values are identical :(
>
> Can you please help?
>
> On Tue, Jun 7, 2011 at 4:02 PM, Thomas Gaillard <
> thomas.gaillard.polytechnique.edu> wrote:
>
>> Le Tuesday 07 June 2011 à 02:33:57PM, Xiao Chen a écrit :
>> > Hi All,
>> >
>> > How can we calculate
>> > a)rmsd of each residue (backbone) at each frame in the simulation
>> (not
>> > r.m.s.f).
>> > b)rmsd of only the side-chain at each frame in the simulation .
>> >
>> > Thanks,
>> >
>> > Po
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> You can do it with ptraj using a script similar to this (adapt the
>> selections to your needs):
>>
>> ptraj file.prmtop << EOF
>> reference ref.pdb
>> trajin traj.crd
>> rms reference out rmsd_bb.dat .N,CA,C
>> rms reference out rmsd_sc.dat !.N,CA,C,O,H
>> go
>> EOF
>>
>> --
>> Thomas Gaillard
>> Maître de conférences
>> Laboratoire de Biochimie
>> Ecole Polytechnique
>> 91128 Palaiseau cedex
>> tel: +33 1 69 33 48 62
>> fax: +33 1 69 33 49 09
>> thomas.gaillard.polytechnique.edu
>> http://bioc.polytechnique.fr/~gaillard
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 07 2011 - 04:30:05 PDT
