From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Oct 10 2013 - 03:49:56 CDT

Firstly: are you sure you want to do that? There's really no conceivable situation in which *both* termini will be uncharged.

Secondly: the approach you're trying won't work. Psfgen has to apply *some* sort of patch in order to define atom types, bonds etc. You'll need patches defining neutral termini. This shouldn't be too difficult - have a look at how neutral glutamic acid (GLUP) and lysine (LYSN, I believe) are defined in the topology file.

Hope this helps.

Cheers,

Tristan



Tristan Croll
Lecturer
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 10 Oct 2013, at 4:39 pm, "Wanzhi Qiu" <wanzhiqiu128_at_yahoo.com<mailto:wanzhiqiu128_at_yahoo.com>> wrote:

Dear All,

I am trying to build a small peptide (GLY-PHE-GLY-GLY, in Alpha helix) ) with N-terminus and C-terminus
in the forms of NH2 and COOH, respectively. The problem is that psfgen forces to apply
the NH3 and COO termini when it is used to generate the corresponding psf file.

The peptide is built with VMD's Protein Builder, the NH2 terminal is automatically there,
and the COOH is creatd by replacing the terminating H atom of the COH in the last GLY
with hydroxyl by Molefacture, all basic and standard operations.

The result is saved as a pdb file, then autopfs is used to generate corresponding psf file. It is
notices that in top_top_all27_prot_lipid_na.inp, the forms of NH3 (GLYP) and COO (CTER)
termini are defined, so that I tried the -noterm option to ask psfhen not to apply termini.
The problem is that, wither with or without the option -noterm, psfgen always creates the NH3 and COO termini.

I did get some warning messages while issuing the command autopsf -mol <MolID> -noterm:

....

psfgen) setting patch for first residue to GLYP
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
segment complete.
psfgen) reading coordinates from pdb file c1_fix_autopsf-temp.pdb_P1.pdb for segment P1
psfgen) Warning: failed to set coordinate for atom O GLY:4 P1
psfgen) Warning: failed to set coordinate for atom O GLY:4 P1
psfgen) Warning: failed to set coordinate for atom H GLY:4 P1
Determine S-S bonds based on distance <3.0A
psfgen) Info: guessing coordinates for 3 atoms (2 non-hydrogen)
psfgen) Warning: poorly guessed coordinates for 3 atoms (2 non-hydrogen):
psfgen) Warning: poorly guessed coordinate for atom HT3 GLY:1 P1
psfgen) Warning: poorly guessed coordinate for atom OT1 GLY:4 P1
psfgen) Warning: poorly guessed coordinate for atom OT2 GLY:4 P1
psfgen) Info: writing psf file c1_fix_autopsf_tmpfile.psf

.....

It can be seen from above that, even with the command -noterm, psfgen seems still applying its defined
termini to the structure..

BTW, I noticed that similar problems were reported in VMD-L, and I applied the suggested
solutions such as in the autopsf GUI, manually set the N terminal patch to NONE (or ACE)
and C terminal patch to NONE (or CT1). Unfortunately none of them worked.

Could someone advise on how to stop psfgen applying its termini such that the desired forms
NH2 and COOH can be preserved. (The peptide pdb file is attached).

Thanks a lot,

W.


<c1_fix.pdb>