AMBER Archive (2009)

Subject: RE: [AMBER] Warning: name change in pdb file residue

From: Duggan, Brendan M. (bmduggan_at_musc.edu)
Date: Thu Mar 05 2009 - 14:42:21 CST

It looks like the creators of your PDB file wanted to number residues to match another protein and your protein has a glycine inserted between residues 183 and 184 of the other sequence. xleap has recognised the discontinuity in the residue numbering and has warned you about what it has done, which is probably what you would have wanted to do in this situation anyway.

brendan

email: bmduggan_at_musc.edu
phone: (843) 792 5029
fax: (843) 792 4322

________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Donald Keidel [dkeidel_at_scripps.edu]
Sent: Thursday, March 05, 2009 2:25 PM
To: amber_at_ambermd.org
Subject: [AMBER] Warning: name change in pdb file residue

Hi,

I have searched the reflector archive and did not find any information
regarding the xleap error I am encountering.

I am trying to load a pdb into leap using the following command:

> prot= loadPdb ./1D6R_r_b_l_b_pqr.pdb
Loading PDB file: ./1D6R_r_b_l_b_pqr.pdb
Warning: name change in pdb file residue 184 ;
 this residue is split into GLY and TYR.
Warning: name change in pdb file residue 188 ;
 this residue is split into GLY and LYS.
Warning: name change in pdb file residue 221 ;
 this residue is split into ALA and GLN.
3 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
  total atoms in file: 4053

When I look back at the original pdb and I look for residue 184, I see
the following:

ATOM 1196 N GLY A 184A 29.963 5.406 183.864 1.00
12.15 N
ATOM 1197 CA GLY A 184A 30.452 6.739 183.548 1.00
15.39 C
ATOM 1198 C GLY A 184A 30.139 7.226 182.126 1.00
17.66 C
ATOM 1199 O GLY A 184A 29.113 6.864 181.578 1.00
14.32 O
ATOM 1200 N TYR A 184 31.014 8.078 181.568 1.00
16.14 N
ATOM 1201 CA TYR A 184 30.795 8.779 180.294 1.00
15.51 C
ATOM 1202 C TYR A 184 31.986 8.707 179.390 1.00
21.20 C
ATOM 1203 O TYR A 184 33.081 9.102 179.769 1.00
21.25 O
ATOM 1204 CB TYR A 184 30.478 10.276 180.539 1.00
12.62 C
ATOM 1205 CG TYR A 184 29.252 10.400 181.437 1.00
18.78 C
ATOM 1206 CD1 TYR A 184 29.344 10.456 182.835 1.00
20.08 C
ATOM 1207 CD2 TYR A 184 27.970 10.360 180.889 1.00
20.46 C
ATOM 1208 CE1 TYR A 184 28.215 10.426 183.658 1.00
17.13 C
ATOM 1209 CE2 TYR A 184 26.824 10.370 181.688 1.00
21.73 C
ATOM 1210 CZ TYR A 184 26.943 10.394 183.077 1.00
22.25 C
ATOM 1211 OH TYR A 184 25.791 10.416 183.833 1.00
20.65 O

The author has identified residue 184 as both a GLY(184A) and TYR(184).
The only difference between them is the numbering of the residue (184A
vs. 184). Is this warning in leap a warning I can overlook or should I
be choosing one of the 2 residues as the residue I load into leap?
Or Can I use both still in xleap with a simple modification to the pdb file?

Thank you for any help you can provide.

Don 

--
"The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or > prot= loadPdb ./1D6R_r_b_l_b_pqr.pdb
Loading PDB file: ./1D6R_r_b_l_b_pqr.pdb
Warning: name change in pdb file residue 184 ;
 this residue is split into GLY and TYR.
Warning: name change in pdb file residue 188 ;
 this residue is split into GLY and LYS.
Warning: name change in pdb file residue 221 ;
 this residue is split into ALA and GLN.
3 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
  total atoms in file: 4053repair."
 -- One of the laws of computers and programming revealed

                                     Douglas Adams in "Mostly Harmless"

_______________________________________________________________________

Donald J. Keidel, Ph.D.
Research Associate
The Scripps Research Institute
3377 N. Torrey Pines Court, Suite 100
La Jolla, CA 92037
mail code: TPC-26
phone:  (858) 784-2842
fax:  (858) 784-2341
dkeidel_at_scripps.edu
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

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