VMD-L Mailing List

From: Pete Kekenes-Huskey (huskeypm_at_gmail.com)
Date: Fri Nov 01 2013 - 11:23:22 CDT

 Hello,

I wanted to create a psf file for a peptide chain fragment. Both the
terminal amide and carbonyl are missing atoms, since the fragment was
created from a non-terminal region.

Psfgen appends missing hydrogens/oxygens, though I’d like to override this
behavior, since I am trying to run MMPBSA using a dcd trajectory file
generated using the original peptide. I have tried commenting out ‘first
ACE’, ‘last CT3’, and ‘guesscoord’) in my tcl script to no avail.

1. is there a recommended way to prevent psfgen from adding atoms

2. is this even recommended (e.g will NAMD complain about the
connectivity)?

Thanks

Pete

Here is an example file:

Test.pdb:

ATOM 1 N MET A 1 36.089 56.723 42.746 0.00 0.00 A

ATOM 2 HT1 MET A 1 35.117 57.093 42.747 0.00 0.00 A

ATOM 3 HT2 MET A 1 35.922 55.714 42.555 0.00 0.00 A

ATOM 4 HT3 MET A 1 36.629 57.054 41.921 0.00 0.00 A

ATOM 5 CA MET A 1 36.735 57.100 44.017 0.00 0.00 A

ATOM 6 HA MET A 1 36.156 56.569 44.758 0.00 0.00 A

ATOM 7 CB MET A 1 38.176 56.450 44.055 0.00 0.00 A

ATOM 8 HB1 MET A 1 38.508 56.334 45.109 0.00 0.00 A

ATOM 9 HB2 MET A 1 38.147 55.408 43.671 0.00 0.00 A

ATOM 10 CG MET A 1 39.254 57.158 43.307 0.00 0.00 A

ATOM 11 HG1 MET A 1 39.029 57.005 42.230 0.00 0.00 A

ATOM 12 HG2 MET A 1 39.171 58.211 43.650 0.00 0.00 A

ATOM 13 SD MET A 1 40.869 56.679 43.910 0.00 0.00 A

ATOM 14 CE MET A 1 41.870 58.118 43.507 0.00 0.00 A

ATOM 15 HE1 MET A 1 41.890 58.857 44.336 0.00 0.00 A

ATOM 16 HE2 MET A 1 42.916 57.964 43.164 0.00 0.00 A

ATOM 17 HE3 MET A 1 41.379 58.618 42.646 0.00 0.00 A

ATOM 18 C MET A 1 36.649 58.644 44.355 0.00 0.00 A

ATOM 19 O MET A 1 37.285 59.434 43.611 0.00 0.00 A

ATOM 20 N ASP A 2 36.001 58.956 45.495 0.00 0.00 A

ATOM 21 HN ASP A 2 35.599 58.273 46.100 0.00 0.00 A

ATOM 22 CA ASP A 2 35.480 60.216 45.745 0.00 0.00 A

ATOM 23 HA ASP A 2 35.400 60.835 44.864 0.00 0.00 A

ATOM 24 CB ASP A 2 34.007 60.119 46.282 0.00 0.00 A

ATOM 25 HB1 ASP A 2 33.484 61.072 46.510 0.00 0.00 A

ATOM 26 HB2 ASP A 2 33.380 59.636 45.503 0.00 0.00 A

ATOM 27 CG ASP A 2 33.911 59.139 47.394 0.00 0.00 A

ATOM 28 OD1 ASP A 2 33.541 59.574 48.534 0.00 0.00 A

ATOM 29 OD2 ASP A 2 34.134 57.903 47.271 0.00 0.00 A

ATOM 30 C ASP A 2 36.421 60.957 46.658 0.00 0.00 A

*My.tcl:*

* *

*set TOPFILE "/Applications/VMD
1.9.1.app/Contents/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/top_all27_prot_lipid.rtf"
*

* *

*package require psfgen*

*topology ${TOPFILE}*

*pdbalias residue HOH TIP3*

* *

*set prot test*

*set name out*

* *

*set S P1*

*segment $S {*

*# first ACE*

* pdb $prot.pdb*

*# last CT3*

*}*

*coordpdb $prot.pdb $S*

* *

*#guesscoord (removing so we don'tadd/remove any atoms)*

*writepdb $name.pdb*

*writepsf $name.psf* 

-- 
======================
Peter Kekenes-Huskey, Ph.D.
Postdoctoral Researcher
UCSD Dept of Pharmacology
4205 Urey Hall
9500 Gilman Avenue
La Jolla, CA 92093
http://mccammon.ucsd.edu/~huskeypm/
======================