VMD-L Mailing List

From: Wanzhi Qiu (wanzhiqiu128_at_yahoo.com)
Date: Thu Oct 10 2013 - 00:11:40 CDT

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.