VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 08 2010 - 19:25:12 CDT

It didn't fail, it just probably didn't do a very good job. However, minimization will fix it very quickly; even using AutoIMD in VMD for a short run would be sufficient.

On Oct 8, 2010, at 11:32 AM, Markus K. Dahlgren wrote:

> 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
>>
>>
>