From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Sep 15 2015 - 17:53:20 CDT
This all looks correct to me. The ACE and CTER patches don't add extra residues, they just modify the existing residues to add extra atoms and change atom types as necessary. This is different to how things are done in the Protein Data Bank, which is where I suspect your confusion arises.
Cheers,
Tristan
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Mona Habibi <monahabibi_at_gmail.com>
Sent: Wednesday, 16 September 2015 6:31 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: NAMD/VMD: generating psf for Abeta, ACE patch
Hello,
I am trying to cap the N-terminus of the first segment of 2BEG (Abeta) protein with ACE and the C-terminus with CTER. I was wondering if the patching has been done correctly. Some conformations at the beginning and end of the segment have been skipped. Also, the name of the N- and C-terminus residues are the same as the first (LEU) and last (ASN) residues, not as ACE and CTER. I would appreciate if anyone can help. Here is my script;
topology top_all27_prot_lipid.inp
segment U {
pdb P1.pdb
first ACE
last CTER
}
coordpdb P1.pdb U
guesscoord
regenerate angles dihedrals
writepdb P1-cap.pdb
writepsf P1-cap.psf
These are the info:
psfgen) setting patch for first residue to ACE
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 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 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.
This is the beginning of the psf file:
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology top_all27_prot_lipid.inp
REMARKS segment U { first ACE; last CTER; auto angles dihedrals }
REMARKS patch ACE U:17
REMARKS patch CTER U:27
In the output pdb file, for the ACE and the first residue I have
REMARK original generated coordinate pdb file
ATOM 1 CAY LEU A 17 -17.210 -5.547 -2.876 0.00 0.00 U C
ATOM 2 HY1 LEU A 17 -17.642 -4.825 -2.336 0.00 0.00 U H
ATOM 3 HY2 LEU A 17 -17.092 -6.367 -2.316 0.00 0.00 U H
ATOM 4 HY3 LEU A 17 -17.772 -5.758 -3.675 0.00 0.00 U H
ATOM 5 CY LEU A 17 -16.312 -5.231 -3.183 0.00 0.00 U C
ATOM 6 OY LEU A 17 -15.880 -5.954 -3.722 0.00 0.00 U O
ATOM 7 N LEU A 17 -16.160 -4.303 -2.843 1.00 0.00 U N
ATOM 8 HN LEU A 17 -16.592 -3.581 -2.303 0.00 0.00 U H
ATOM 9 CA LEU A 17 -14.856 -3.844 -3.289 1.00 0.00 U C
and this is for the end terminus
ATOM 161 OD1 ASN A 27 16.452 -8.886 0.333 1.00 0.00 U O
ATOM 162 ND2 ASN A 27 18.094 -8.793 -1.205 1.00 0.00 U N
ATOM 163 HD21 ASN A 27 18.701 -8.210 -1.745 1.00 0.00 U H
ATOM 164 HD22 ASN A 27 18.140 -9.787 -1.302 1.00 0.00 U H
ATOM 165 C ASN A 27 15.804 -4.728 -0.190 1.00 0.00 U C
ATOM 166 OT1 ASN A 27 14.907 -4.677 -0.629 0.00 0.00 U O
ATOM 167 OT2 ASN A 27 16.610 -4.175 0.022 0.00 0.00 U O
The N- and C-terminus are shown in bold.
Regards,
Mona
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