Hi Carlos,
Thanks for that tip!
Do you mean I should do the following?
reference reference_structure.pdb :1-290
rms reference mass :1-289
rms reference mass out ligand_rmsd.dat :290 nofit
or:
reference reference_structure.pdb :1-289
rms reference mass :1-289
reference reference_structure.pdb :290
rms reference mass out ligand_rmsd.dat :290 nofit
Yingjie
On Apr 27, 2010, at 9:14 PM, Carlos Simmerling wrote:
> do this in 2 steps. first, align the protein using an rms command and mask
> for the protein.
> then do another rms command, for the ligand only, but put "nofit" at the end
> of the line.
>
>
> On Tue, Apr 27, 2010 at 8:42 PM, Yingjie Lin <linyj1984.gmail.com> wrote:
>
>> Dear all,
>>
>> I've run 30ns simulation of a protein-ligand complex.
>> The protein has 289 residues, and the 290th "residue" corresponds to the
>> ligand.
>>
>> I am interested in checking how the ligand move in the simulation.
>> To be more specific, I would like to calculate RMSD of the ligand with
>> respect to the ligand in another file (named fileA.pdb).
>>
>> My script looks like this:
>> =======
>> trajin ../EQ/complex.1.trj.gz 1 1000 25
>> trajin ../EQ/complex.2.trj.gz 1 1000 25
>> ...
>>
>> center origin :1-290
>> image origin center
>>
>> rms first mass out complex_rmsf_ca.dat .CA
>>
>> strip :291-119999999
>>
>> reference fileA.pdb :1-290
>> rms reference mass out ligand_rmsf.dat :290
>> ======
>> I am not sure about the last two lines. Since I want to "align the protein
>> and then calculate RMSD for the ligand",
>> which of the following should I use?
>> 'reference fileA.pdb :1-290'
>> or 'reference fileA.pdb :1-289'
>> or 'reference fileA.pdb :290'
>>
>>
>> Thanks a lot!
>>
>> Yingjie
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Received on Wed Apr 28 2010 - 08:00:04 PDT
