VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Aug 24 2017 - 18:30:23 CDT

Hi Arthur,

Naw. "type" in VMD is for the atomtype (parameter type), which for
lipids are things like CTL, CEL1, and CEL3. Apparently CHARMM calls them
"chem". This is DIFFERENT than "name", assuming you've loaded your psf
first... Oh wait. This is probably a CHARMM-format psf, with numbers as
the type. From CHARMM-GUI, you want the .xplor.psf (which has atomtypes
like CEL1), not the .psf (which *might* have numeric atomtypes). Look,
this is all really easy to check with VMD. Just see what is displayed
with a test selection string! I'm certain the equivalent text is "type CEL1"

-Josh

On 08/24/2017 05:17 PM, Arthur Vale wrote:
> 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
>
>