VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sun Feb 08 2015 - 19:30:28 CST

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