VMD-L Mailing List

From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Thu Oct 07 2010 - 15:11:52 CDT

I am trying to patch single amino acid residues with the CT3 (N-methylamide
C-terminus) and ACE (acetylated N-terminus). I have been trying to patch
alanine. I have attached the pdb input file below.

REMARK original generated coordinate pdb file
ATOM 1 N ALA X 1 3.577 3.946 0.006 1.00 0.00 P1 N
ATOM 2 HT1 ALA X 1 3.710 3.108 -0.523 1.00 0.00 P1 H
ATOM 3 HT2 ALA X 1 2.909 4.535 -0.450 1.00 0.00 P1 H
ATOM 4 HT3 ALA X 1 3.261 3.721 0.928 1.00 0.00 P1 H
ATOM 5 CA ALA X 1 4.846 4.653 0.100 1.00 0.00 P1 C
ATOM 6 HA ALA X 1 5.593 4.080 0.637 1.00 0.00 P1 H
ATOM 7 C ALA X 1 4.614 5.931 0.914 1.00 0.00 P1 C
ATOM 8 OT1 ALA X 1 3.477 6.389 1.041 1.00 0.00 P1 O
ATOM 9 OT2 ALA X 1 5.691 6.517 1.445 1.00 0.00 P1 O
ATOM 10 CB ALA X 1 5.339 4.991 -1.317 1.00 0.00 P1 C
ATOM 11 HB1 ALA X 1 5.548 4.052 -1.873 1.00 0.00 P1 H
ATOM 12 HB2 ALA X 1 4.569 5.559 -1.883 1.00 0.00 P1 H
ATOM 13 HB3 ALA X 1 6.274 5.591 -1.293 1.00 0.00 P1 H
END

When I apply the two patches in TKconsole I get these messages:

>Main< (ala) 4 % patch CT3 P1:1
applying patch CT3 to 1 residues
no atom O in residue ALA:1 of segment P1
Warning: add improper failed in patch CT3
no atom O in residue ALA:1 of segment P1
Warning: add conformation failed in patch CT3
no atom O in residue ALA:1 of segment P1
Warning: add conformation failed in patch CT3

>Main< (ala) 5 % patch ACE P1:1
applying patch ACE to 1 residues
no atom HN in residue ALA:1 of segment P1
Warning: add improper failed in patch ACE
no atom HN in residue ALA:1 of segment P1
Warning: add conformation failed in patch ACE

I have tried to rename HT3 to HN and also OT2 to O. That does not solve the
problem. I do not know how to apply these two patches two my amino acids. On a
sidenote I did not have any problems at any stage to apply the CTER and NTER
patches. Any help would be greatly appreciated!!

/Markus