VMD-L Mailing List

From: Arthur Vale (arthurovale_at_uchicago.edu)
Date: Thu Aug 24 2017 - 18:17:29 CDT

Hi Josh!

I believe that indeed, "type" in charmm is the same as "name" in tcl/vmd. But in Charmm there are selections like "chem CTL2 .or. chem CEL1 .or. chem CEL3" which I'm not sure how to translate to vmd. In some Charmm forum thread I found the following:

"define unsat sele atom D 1 C2_at_C .and. chem CEL1 end
what is the meaning of 1, chem and CEL1?

Another atom selection issue (select.doc); the CHEM token allows one to select atoms based on their parameter type, rather than a IUPAC style label. The CEL1 parameter type is specific for a C atom involved in a C=C double bond."

In any case, your suggestion is neat, but I'm still unsure if those two selections are the same, since I couldn't find any documentation on what the CEL1, CTL2, CEL3, and so on actually mean.

Thank you,

Arthur

________________________________________
From: Vermaas, Joshua [Joshua.Vermaas_at_nrel.gov]
Sent: Thursday, August 24, 2017 6:11 PM
To: Arthur Vale; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Selection Text for two C atoms with a double bond

You mean text like "type CEL1 CEL3"? Or is CHARMM literally looking at topologies rather than the atomtype? In VMD, you could identify sp2 carbons regardless of their atomtype with something like: "name \"C.*\" and numbonds == 3"

-Josh

On 08/24/2017 05:06 PM, Arthur Vale wrote:
Specifically I want to substitute selection texts such as "chem cel1", "chem cel3", "chem cl" and so on that are possible in Charmm for some tcl/vmd equivalent if possible.

-Arthur
________________________________
From: Arthur Vale
Sent: Thursday, August 24, 2017 4:55 PM
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Selection Text for two C atoms with a double bond

Dear All,

Charmm has a nice selection text that allows one to select all C=C pairs (two carbons with a double bond). Is there any way to do this is tcl/vmd?

Thank you in advance,

Arthur