Hi,
Actually the command syntax I gave is for Cpptraj (not Ptraj). Cpptraj
is a new analysis program written in C++ that is included in
AmberTools 1.5. If you would like to use cpptraj you should upgrade to
AT 1.5 (it's free). Upgrading might be a good idea anyway, as there
have been improvements across the entire AmberTools codebase.
Let me know if you have any more questions.
-Dan
On Wed, Jun 8, 2011 at 12:55 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Thanks Dan!
>
> The syntax of the rmsd command as you suggested does not work :(
> Did you mean :
>
> rms :10-260 reference perres range 10-260 perresout PerResRMSD.dat
>
>
> The Amber11 manual has no mention of the perres keyword so im having a tough
> time figuring this out. Could you please help out because your description
> of the output (Each column in that file will be the RMSD of a residue) is
> exactly what i need.
>
> Yours,
>
> Po
>
>
>
> On Tue, Jun 7, 2011 at 4:37 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> If you would like the RMSD of each individual residue after fitting on
>> a larger selection this can be done by Cpptraj. Here is an example
>> input:
>>
>> parm prmtop
>> reference inpcrd
>> trajin mdcrd
>> rmsd :10-260 reference perres range 10-260 perresout PerResRMSD.dat
>>
>> This will first perform an overall rms fit of each frame using
>> residues 10 to 260, then the rmsd of each individual residue in the
>> range of 10 to 260 will be output to PerResRMSD.dat. Each column in
>> that file will be the RMSD of a residue. By default the entire residue
>> is selected; to modify the selection you can specify "perresmask
>> <mask>". For example, to select only backbone atoms of each residue in
>> the above example:
>>
>> rmsd :10-260 reference perres range 10-260 perresout PerResRMSD.dat
>> perresmask &.C,CA,N
>>
>> See the manual for more details and keywords, and let me know if you
>> have trouble getting it to work.
>>
>> -Dan
>>
>> On Tue, Jun 7, 2011 at 5:03 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
>> > 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
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Wed Jun 08 2011 - 06:00:05 PDT
