[Chimera-users] Atom does not have a type
Eric Pettersen
pett at cgl.ucsf.edu
Tue Oct 23 12:40:47 PDT 2007
Hi Francesco,
As I thought might be the case and mentioned in the previous mail,
Amber expects protonated aspartic/glutamic acids to have the proton
attached to the other oxygen. What you need to do is simply swap the
names of the oxygens in these residues and also change the '1' in the
proton name to '2'.
You were right to break the long bonds, but breaking the bonds turns
the formerly connected residues into terminal residues, which means
you need an additional oxygen on the 'C' and two additional hydrogens
on the 'N'. In addition the hydrogen already attached to 'N' now has
the wrong name, since the three hydrogens connected to an N terminus
are named H1, H2, and H3, not H. Probably the simplest way to
resolve this situation is to run your structure through Dock Prep
again (which will fix up the mangled terminii) and write a new PDB
file. Also, you will need to delete the unwanted N-terminal 'H'
hydrogens before running Dock Prep. You can either just delete them
from your input file or use the command 'del :334,223,112,1 at H'.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu
On Oct 23, 2007, at 10:33 AM, Francesco Pietra wrote:
> Thanks to Eric Pettersen I have fixed problems of long bonds and
> mis-assignement by prepare_amber.pl (from HIS to HIE, while it is
> HID).
>
> Two types of problems remain because I was either unable to correct
> or did
> wrongly. The error log from attempted fixing problems:
> WARNING: The unperturbed charge of the unit: 24.000000 is not zero.
> FATAL: Atom .R<GLH 443>.A<HE1 17> does not have a type.
> FATAL: Atom .R<ASH 402>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 386>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 375>.A<HD1 14> does not have a type.
> FATAL: Atom .R<GLH 373>.A<HE1 17> does not have a type.
> FATAL: Atom .R<NSER 334>.A<H 14> does not have a type.
> FATAL: Atom .R<GLH 332>.A<HE1 17> does not have a type.
> FATAL: Atom .R<ASH 291>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 275>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 264>.A<HD1 14> does not have a type.
> FATAL: Atom .R<GLH 262>.A<HE1 17> does not have a type.
> FATAL: Atom .R<NSER 223>.A<H 14> does not have a type.
> FATAL: Atom .R<GLH 221>.A<HE1 17> does not have a type.
> FATAL: Atom .R<ASH 180>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 164>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 153>.A<HD1 14> does not have a type.
> FATAL: Atom .R<GLH 151>.A<HE1 17> does not have a type.
> FATAL: Atom .R<GLH 128>.A<HE1 17> does not have a type.
> FATAL: Atom .R<NSER 112>.A<H 14> does not have a type.
> FATAL: Atom .R<GLH 110>.A<HE1 17> does not have a type.
> FATAL: Atom .R<ASH 69>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 53>.A<HD1 14> does not have a type.
> FATAL: Atom .R<ASH 42>.A<HD1 14> does not have a type.
> FATAL: Atom .R<GLH 40>.A<HE1 17> does not have a type.
> FATAL: Atom .R<GLH 17>.A<HE1 17> does not have a type.
> FATAL: Atom .R<NSER 1>.A<H 14> does not have a type.
>
> UNABLE : I don't know how to rename the hydrogen on serine
> nitrogen. In my
> protein.pdb, the section around residues 333/334:
>
> ATOM 5155 O THR X 333 15.694 -15.150 25.132 0.00
> 0.00 O
> TER 5156 THR X 333
> ATOM 5157 N SER X 334 -16.176 22.312 10.940 0.00
> 0.00 N
> ATOM 5158 H SER X 334 -15.301 22.760 10.966 0.00
> 0.00 H
> ATOM 5159 CA SER X 334 -16.224 20.932 11.429 0.00
> 0.00 C
> ATOM 5160 HA SER X 334 -17.198 20.770 11.905 0.00
> 0.00 H
> ATOM 5161 CB SER X 334 -15.868 19.959 10.306 0.00
> 0.00 C
> ATOM 5162 HB2 SER X 334 -15.761 18.918 10.709 0.00
> 0.00 H
> ATOM 5163 HB3 SER X 334 -14.903 20.280 9.956 0.00
> 0.00 H
> ATOM 5164 OG SER X 334 -16.906 19.973 9.300 0.00
> 0.00 O
> ATOM 5165 HG SER X 334 -16.948 20.844 8.983 0.00
> 0.00 H
> ATOM 5166 C SER X 334 -15.185 20.856 12.533 0.00
> 0.00 C
> ATOM 5167 O SER X 334 -14.212 21.643 12.566 0.00
> 0.00 O
>
> Actually, I only inserted "TER" (where it is now) between residue
> 333 and 334
> to get rid of a long bond between the two; numbering and THR X 333
> came out
> automatically. Also, automatically the pdb file now begins with a
> series of
> HELIX.
>
> BADLY DONE: to correct for the carboxyl hydrogen being on the wrong
> oxygen of
> ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the
> section
>
> ATOM 6851 CD GLU X 443 -10.347 20.009 21.724 0.00 0.00
> ATOM 6852 OE1 GLU X 443 -10.341 20.227 23.079 0.00 0.00
> ATOM 6853 OE2 GLU X 443 -10.192 20.919 20.907 0.00 0.00
> ATOM 6854 HE1 GLU X 443 -10.239 21.145 23.232 0.00 0.00
>
> was rewritten by exchanging two lines, which automatically were
> renumbered
>
> ATOM 6854 CD GLH X 443 -10.347 20.009 21.724 0.00
> 0.00 C
> ATOM 6855 OE1 GLH X 443 -10.341 20.227 23.079 0.00
> 0.00 O
> ATOM 6856 OE2 GLH X 443 -10.192 20.919 20.907 0.00
> 0.00 O
> ATOM 6857 HE1 GLH X 443 -10.239 21.145 23.232 0.00
> 0.00 H
> ATOM 6858 C GLH X 443 -13.205 16.911 22.895 0.00
> 0.00 C
>
> and the issue on prepare_amber.pl was not resolved.
>
> It is obvious that I am carrying out such adjustments for the first
> time. I got
> the impression that from now on, what I do increases the mess.
>
> Must say that with my imperfect pdb I could carry outt all DOCK
> tutorials,
> except the amber_score.
>
> Thanks
> francesco pietra
>
>
>
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