Re: change segID using segment command in psfgen

From: Low Soo Mei (lowsm_at_bii.a-star.edu.sg)
Date: Thu Mar 06 2008 - 19:33:33 CST

>
> Changing the segname from DMPG to DPPC will not
> actually change anything about the structure (I'm not sure if this is what
> you were intending).

Yes. I understand that. But thank you for the clarification as well.

What I truly needed to do was to rename the segnames of some identical
protein chains in my concatenated pdb so that I could identify them
separately in VMD. For this instance, the "$sel set segname DPPC" would
not work because it would affect all the chains. But it is a cool
command that I did not know about previously. Thanks again.

Cheers,
Soo Mei

JC Gumbart wrote:
> " Or should the changing of
> segID indeed be done using the segment command?"
>
> Yes.
>
> Psfgen generates the segment based on the segment command. Then coordpdb
> adds the coordinates to that segment. Coordpdb doesn't care what the
> segment name is in the pdb file, but if the name doesn't match that used in
> the segment command, it will have no idea what to do.
>
> In VMD, you can also easily change segment names. Just make an atom
> selection like "segname DMPG" and then do "$sel set segname DPPC".
>
> Just to be absolutely clear, the segname is just an identifier and is not
> interpreted to hold any specific chemical information about the system
> (unlike the resname). Changing the segname from DMPG to DPPC will not
> actually change anything about the structure (I'm not sure if this is what
> you were intending).
>
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Low Soo Mei
> Sent: Thursday, March 06, 2008 3:01 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: change segID using segment command in psfgen
>
> Dear NAMD users,
>
> This is not a scientific query, but a scripting query. I would like to
> ask: The NAMD 2.6 (latest) user guide pg 39 says that the coordpdb
> command in the psfgen package can "override segment IDs in PDB file".
> However, when I used that to try to override my input PDB file's segID,
> it did not work, as below.
>
> topology toppar/top_all22_prot.inp
> segment DMPG {
> pdb membrane.pdb
> }
> coordpdb membrane.pdb DPPC
> (massive error output for every atom, saying "no segment DPPC found")
>
>
> When I instead specified the new segID I wanted using the segment
> command, during the 'Build protein segment' part and inspected the
> output mem_test psf and pdb files in vi, it seems to have worked, as below.
>
> topology toppar/top_all22_prot.inp
> segment DPPC {
> pdb membrane.pdb
> }
> coordpdb membrane.pdb DPPC
> (no error output)
> guesscoord
> writepsf mem_test.psf
> writepdb mem_test.pdb
>
>
> Have I perhaps been using coordpdb wrongly? Or should the changing of
> segID indeed be done using the segment command?
>
> I have been trying to find a general way to change the segID within VMD
> instead of doing it by hand, for some time.
>
> Many thanks for your advice.
>
> Cheers,
> Soo Mei
>

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