VMD-L Mailing List

From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Feb 09 2015 - 02:28:54 CST

Tristan, I think that is the only way, my only issue was I didn't want the
peptides to be very close as I was interested in their studying their
interaction after certain period. Fortunately, there are commands by which
we can displace the peptides by a desired amount, save it as a separate
.pdb file and combine as you have shown. The link below provides ample
information on that:

http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node181.html#14132

Regards
Sourav

On Mon, Feb 9, 2015 at 7:00 AM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:

> True enough - but it's a useful skill to learn. Sourav, try this:
>
>
> If this is the PDB file of your first peptide:
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 N PRO A 3 -1.476 22.981 -56.671 1.00 1.00
> AP1 N
> ATOM 2 HN1 PRO A 3 -1.217 23.905 -56.972 1.00 1.00
> AP1
> ATOM 3 HN2 PRO A 3 -1.397 22.948 -55.669 1.00 1.00
> AP1
> ATOM 4 CD PRO A 3 -2.887 22.696 -57.106 1.00 1.00
> AP1 C
> ...
> ATOM 8639 HG2 GLU A 590 -5.112 47.887 -19.024 1.00 1.00
> AP5
> ATOM 8640 CD GLU A 590 -4.262 45.936 -19.414 1.00 1.00
> AP5
> ATOM 8641 OE1 GLU A 590 -3.791 45.667 -18.277 1.00 1.00
> AP5
> ATOM 8642 OE2 GLU A 590 -4.589 45.062 -20.261 1.00 1.00
> AP5
> END
>
> ... and this is the PDB file of your second:
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 8643 N ARG C 2 10.212 48.837 -61.346 1.00 1.00
> CP1 N
> ATOM 8644 HT1 ARG C 2 9.211 48.805 -61.629 1.00 1.00
> CP1
> ATOM 8645 HT2 ARG C 2 10.813 48.624 -62.168 1.00 1.00
> CP1
> ATOM 8646 HT3 ARG C 2 10.441 49.783 -60.982 1.00 1.00
> CP1
> ...
> ATOM 8807 CD GLN C 10 20.274 59.794 -61.815 1.00 1.00
> CP1 C
> ATOM 8808 OE1 GLN C 10 19.392 58.948 -61.990 1.00 1.00
> CP1 O
> ATOM 8809 NE2 GLN C 10 21.601 59.487 -61.707 1.00 1.00
> CP1 N
> ATOM 8810 HE21 GLN C 10 21.898 58.534 -61.769 1.00 1.00
> CP1
> ATOM 8811 HE22 GLN C 10 22.272 60.215 -61.568 1.00 1.00
> CP1
> END
>
>
> Just copy-paste everything but the CRYST1 and END lines from the second to
> the first so that the end result looks like this, and save as a new file.
> AutoPSF will know what to do with it from here.
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 N PRO A 3 -1.476 22.981 -56.671 1.00 1.00
> AP1 N
> ATOM 2 HN1 PRO A 3 -1.217 23.905 -56.972 1.00 1.00
> AP1
> ATOM 3 HN2 PRO A 3 -1.397 22.948 -55.669 1.00 1.00
> AP1
> ATOM 4 CD PRO A 3 -2.887 22.696 -57.106 1.00 1.00
> AP1 C
> ...
> ATOM 8639 HG2 GLU A 590 -5.112 47.887 -19.024 1.00 1.00
> AP5
> ATOM 8640 CD GLU A 590 -4.262 45.936 -19.414 1.00 1.00
> AP5
> ATOM 8641 OE1 GLU A 590 -3.791 45.667 -18.277 1.00 1.00
> AP5
> ATOM 8642 OE2 GLU A 590 -4.589 45.062 -20.261 1.00 1.00
> AP5
> ATOM 8643 N ARG C 2 10.212 48.837 -61.346 1.00 1.00
> CP1 N
> ATOM 8644 HT1 ARG C 2 9.211 48.805 -61.629 1.00 1.00
> CP1
> ATOM 8645 HT2 ARG C 2 10.813 48.624 -62.168 1.00 1.00
> CP1
> ATOM 8646 HT3 ARG C 2 10.441 49.783 -60.982 1.00 1.00
> CP1
> ...
> ATOM 8807 CD GLN C 10 20.274 59.794 -61.815 1.00 1.00
> CP1 C
> ATOM 8808 OE1 GLN C 10 19.392 58.948 -61.990 1.00 1.00
> CP1 O
> ATOM 8809 NE2 GLN C 10 21.601 59.487 -61.707 1.00 1.00
> CP1 N
> ATOM 8810 HE21 GLN C 10 21.898 58.534 -61.769 1.00 1.00
> CP1
> ATOM 8811 HE22 GLN C 10 22.272 60.215 -61.568 1.00 1.00
> CP1
> END
>
>
>
> You will of course want to get them aligned more or less as you want
> them before writing the initial PDB files. I find the Mouse/Move/Rep
> (hotkey 9) tool to be particularly useful here - it will allow you to move
> only the atoms in the representation you currently have selected in the
> Graphical Representations window.
>
>
> Cheers,
>
>
> Tristan
>
>
>
> ------------------------------
> *From:* Richard Wood <Richard.Wood_at_purduecal.edu>
> *Sent:* Monday, 9 February 2015 11:11 AM
> *To:* Tristan Croll; Sourav Ray; vmd-l_at_ks.uiuc.edu
> *Subject:* RE: vmd-l: Putting different peptide chains (spaced apart) in
> a single .xbgf file
>
> Not many ppl know how to get under the hood of a pdb file...
>
> Richard
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Tristan Croll [tristan.croll_at_qut.edu.au]
> *Sent:* Sunday, February 08, 2015 2:57 PM
> *To:* Sourav Ray; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Putting different peptide chains (spaced apart) in
> a single .xbgf file
>
> I think your best option is to write each peptide to a PDB file and
> then just put them together using a text editor. As long as you give each
> peptide a different chain name VMD is very tolerant in this way - just
> copy-paste all the ATOM lines from one PDB file to the other (before the
> final END statement).
>
>
> Cheers,
>
>
> Tristan
>
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Sourav Ray <souravray90_at_gmail.com>
> *Sent:* Wednesday, 4 February 2015 9:25 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Putting different peptide chains (spaced apart) in a
> single .xbgf file
>
> Hello
>
> With the help of Extensions -> Modeling -> Molefacture -> Start
> Molefacture -> Protein Builder -> Build. I can create a single
> peptide/protein chain of desired number of amino acids. However, I am not
> being able to insert multiple peptides in a single .xbgf file so that I can
> later save the coordinates as a .pdb file later. Actually I want to study
> peptide interaction. Kindly let me know if there is some way I can do that
> here or any alternative method that can be employed.
>
> Thanks
> Sourav
>