VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Aug 04 2007 - 12:04:20 CDT

Hi Francesco,
coloring by Element rather than Name should behave as you want, then.
You may want to give that a try to see whether the chlorine atoms are
properly marked as such. I'm not familiar with amber file formats or the
vmd molfile plugins for them, so I'm not sure how much information on
the element of each atom is available. What is the file format of that
topology file you're using?

Peter

Francesco Pietra wrote:
> Dear Peter:
> Thanks. "not resname CL3" works.
>
> The file is named frcmod.chcl3, where atom names for carbon, chlorine, and
> hydrogen are CZ, CL, HZ, in the order. There, MASS, BOND, ANGL, and NONB are
> assigned.
>
> I have now "experimented" that:
>
> "all not type CL" removes the three chlorine atoms from all chloroform
> molecules in the box. Analogously for carbon and hydrogen of the solvent with
> CZ and HZ.
>
> For the solute (a methylcyclohexane, hope you are not disappointed by the
> simplicity of the trials I am carrying out) "all not type c3" or "all not type
> hc" work nicely.
>
> In summary, what remains open, is distinguishing by color chloroform from
> carbon, although the "type' command shows where chlorines are.
>
> Regards
>
> francesco
>
>
> --- Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
>
>> Hi Francesco,
>> hiding the chloroform to see the solute should be easy enough if you
>> make your graphical representation
>> "not resname XXX" (where XXX is whatever residue name chloroform has in
>> your system).
>>
>> When VMD reads a structure, it has several steps that it goes through to
>> try to assign elements to each atom. The first (and most obvious) is
>> that some file formats actually carry element names or numbers;
>> sometimes it has to fall back to guessing based on atom name, which is
>> probably what is going on here -- atoms named Csomething are being IDed
>> as carbon instead of chlorine. What type of file are you reading in to
>> provide the topology information for your structure? And what atom name
>> do your chlorine atoms have?
>>
>> Best,
>> Peter
>>
>> Francesco Pietra wrote:
>>
>>> Dealing with a chloroform box from Amber9, I was unable to hide the
>>>
>> chloroform
>>
>>> molecules in order to see the solute better.
>>>
>>> Curiously, if I set to show carbon only, this is performed correctly for
>>>
>> the
>>
>>> solute molecule, while chloroform is shown as an ammonia-like
>>> umbrella with four identical atoms. I.e., chlorine is shown as if it were
>>> carbon. I was unable to trace where to deal with chlorine atom.
>>>
>>> Thanks for help
>>>
>>> francesco pietra
>>>
>>>
>>>
>>>
>>>
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