VMD-L Mailing List

From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Fri Oct 08 2010 - 11:32:02 CDT

I tried applying the patch using the first and last commands in the segment
section. The correct atom names are assigned, but the coordinates are all
messed up. Guesscoord fails to guess the coordinates. Is there a better way of
taking a single amino acid reside and cap it with the ACE and CT3?

/Markus

> Main< (ala) 9 % segment P1 {pdb ala_mod.pdb
first ACE
last CT3
}
building segment P1
reading residues from pdb file ala_mod.pdb
extracted 1 residues from pdb file
setting patch for first residue to ACE
setting patch for last residue to CT3
Info: generating structure...
Info: skipping bond C-N at beginning of segment.
Info: skipping improper O-C-CA-N at beginning of segment.
Info: skipping improper HN-N-C-CA at beginning of segment.
Info: skipping conformation CA-C-N-CA at beginning of segment.
Info: skipping conformation N-CA-C-O at beginning of segment.
Info: skipping conformation N-CA-C-N at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: segment complete.
> Main< (ala) 10 % coordpdb ala_mod.pdb
reading coordinates from pdb file ala_mod.pdb
Warning: failed to set coordinate for atom OT1 ALA:1 P1
Warning: failed to set coordinate for atom OT2 ALA:1 P1
> Main< (ala) 11 % guesscoord
Info: guessing coordinates for 11 atoms (6 non-hydrogen)
Warning: poorly guessed coordinates for 11 atoms (6 non-hydrogen):
Warning: poorly guessed coordinate for atom NT ALA:1 P1
Warning: poorly guessed coordinate for atom HNT ALA:1 P1
Warning: poorly guessed coordinate for atom CAT ALA:1 P1
Warning: poorly guessed coordinate for atom CAY ALA:1 P1
Warning: poorly guessed coordinate for atom HY1 ALA:1 P1
Warning: poorly guessed coordinate for atom HY2 ALA:1 P1
Warning: poorly guessed coordinate for atom HY3 ALA:1 P1
Warning: poorly guessed coordinate for atom CY ALA:1 P1
Warning: poorly guessed coordinate for atom OY ALA:1 P1
Warning: poorly guessed coordinate for atom HN ALA:1 P1
Warning: poorly guessed coordinate for atom O ALA:1 P1
> Main< (ala) 12 % writepdb ala_capped.pdb
Info: writing pdb file ala_capped.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
> Main< (ala) 13 %

Quoting JC Gumbart <gumbart_at_ks.uiuc.edu>:

> Instead of applying the patch after the fact, try adding "first ACE"
> and "last CT3" within your segment command. The problem is that a
> given segment is terminated with NTER and CTER by default, unless you
> tell it otherwise.
>
>
> On Oct 7, 2010, at 3:11 PM, Markus K. Dahlgren wrote:
>
>> 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
>
>