VMD-L Mailing List

From: Pete Kekenes-Huskey (huskeypm_at_gmail.com)
Date: Mon Nov 04 2013 - 15:42:49 CST

Hi Josh,
This did the trick! Thank you for such an easy solution.
Best,
pete

On Fri, Nov 1, 2013 at 11:01 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Pete,
> Have you tried "first none" and "last none"? I believe the default patch
> for protein segments is first NTER last CTER if you don't override it,
> which would add the usual N and C terminus. If you just need a psf for a
> protein fragment because a tool needs ones, I'd select a subset with
> something like:
>
> set mid [mol new originalfile.psf]
> set sel [atomselect $mid "resid 1 to 2"]
> $sel writepsf selection.psf
>
> rather than messing with psfgen. The one caveat to this approach is that
> it doesn't work with 1.9.1 if you have atomtypes longer than 4 charachters,
> but for just a peptide in water, that shouldn't be an issue.
>
> -Josh
>
>
> On 11/01/2013 11:23 AM, Pete Kekenes-Huskey wrote:
>
> 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/
> ======================
>
>
> 

-- 
======================
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/
======================