AMBER Archive (2009)

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

From: Donald Keidel (dkeidel_at_scripps.edu)
Date: Thu Mar 05 2009 - 13:25:38 CST

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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