On Thu, Jan 12, 2017 at 12:11 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> parm file.prmtop
> trajin reimaged.mdcrd
> rms ToFirst :297&!.H= first out rmsd1.agr
If your goal is to look at the RMSD of residue 297 (no hydrogens) with
respect to the first frame, this is fine.
-Dan
>
> Is it fine?
>
>
>
> On Wednesday, January 11, 2017 7:46 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>
> First, I *strongly* recommend you read the cpptraj section of the
> Amber 16 manual; in particular look up the commands you are using and
> make sure you understand what each is doing.
>
> On Wed, Jan 11, 2017 at 6:11 AM, Saman Yousuf ali
> <saman.yousufali64.yahoo.com> wrote:
>> Dear All,I need a cpptraj script to calculate rmsd of ligand throughout
>> md. I searched some tutorial in which following script for used for
>> plotting ligand rmsd; parm file.prmtop
>> trajin reimaged.mdcrd
>> rms first :297.C*,N*,O*,S*,F*,Cl* out rmsd.datstrip :WAT
>
> You specified two masks; if you look at the manual entry for the
> 'rmsd' command you will see that the first mask selects atoms in your
> frames (i.e. the target atoms), while the second mask selects atoms in
> your reference structure. So what you've told cpptraj to do here is
> calculate the RMSD of all atoms selected by C*, N*, O*, S*, F*, and
> Cl* in residue 297 for frames read in from 'reimaged.mdcrd' to all
> atoms selected by :WAT (i.e. all water atoms) in the first frame. This
> is almost certainly not what you want to do.
>
>
>> strip :Na+
>
>
> Unless you will be writing out a trajectory or doing some other kind
> of action, this 'strip' command seems pointless to me.
>
> Again, please read the manual to try and understand the commands you
> are using. You may also find the following tutorial helpful:
> http://ambermd.org/tutorials/analysis/tutorial1/
>
> -Dan
>
> --
> -------------------------
> 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
>
>
>
--
-------------------------
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 Thu Jan 12 2017 - 06:30:02 PST
