NAMD/VMD: generating psf for Abeta, ACE patch

From: Mona Habibi (monahabibi_at_gmail.com)
Date: Tue Sep 15 2015 - 15:31:37 CDT

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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