VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Thu Jan 17 2008 - 14:45:04 CST

Hi,

just use "resname xxx and name c o1 n4"
with c, o1 and n4 being the atom names.

Best,
Luis

Francesco Pietra said the following on 01/17/2008 12:11 PM:
> Hi Luis:
> I forgot to ask in my previous mail: While for the protein I use ff99SB, for
> the single residue ligand I use GAFF. That means that atom names are in small
> case (otherwise corresponding to the upper case of ff99SB). I would like to
> limit RMSD to certain atoms, especially the ethereal oxygen atom of the ligand.
>
> Thanks
> francesco
>
>
>
>
> --- Luis Gracia <lug2002_at_med.cornell.edu> wrote:
>
>
>> Hi Francesco,
>>
>> make sure 'Trace' is not active in the atom selection box. For more
>> information about all the options take a look here:
>>
>>
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/#options
>
>> Best,
>> Luis
>>
>> Francesco Pietra said the following on 01/17/2008 01:49 AM:
>>
>>> I am carrying out MD of a protein-ligand (the latter non polymeric, large)
>>>
>> in a
>>
>>> POPC membrane. Things run satisfactorily, though I was unable to gather all
>>> information that should be possible.
>>>
>>> The ligand has O-hetero-rings, so that in visualizing rmsd with the RMDS
>>>
>> traj
>>
>>> Tool I would like to have the oxygen atom included. What I did in the
>>>
>> window
>>
>>> was to replace on top left box "protein" with "resname XYZ", where XYZ is
>>>
>> the
>>
>>> name of the ligand. I got the plot with the top indication (in red) "RMSD
>>>
>> vs
>>
>>> Frame "(resname XYZ) and name C CA N". This ligand has no aromatic carbons,
>>>
>> nor
>>
>>> nitrogen atoms. It has sp3 and sp2 carbons and ethereal oxygen. Where
>>>
>> should I
>>
>>> set these indications?
>>>
>>> I know I should educate myself throughly on VMD. Time is short.
>>>
>>> Thanks
>>> francesco pietra
>>>
>>>
>>>
>>>
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