Thanks! Good catch.
Mike
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Ross Walker
Sent: Monday, July 06, 2009 9:29 PM
To: 'AMBER Mailing List'
Subject: RE: [AMBER] Tleap input error, atom not found in residue template
Hi Mike,
So I tried this out with your pdb and I get:
Created a new atom named: H within residue: .R<NTYR 1>
total atoms in file: 246
Leap added 3 missing atoms according to residue templates:
3 H / lone pairs
So the problem is with your N terminal Tyrosine. In your pdb you have:
ATOM 1 N TYR A 1 -0.655 -2.299 1.364 1.00 0.00
N
ATOM 2 CA TYR A 1 -0.404 -1.281 0.350 1.00 0.00
C
ATOM 3 C TYR A 1 0.913 -1.591 -0.381 1.00 0.00
C
ATOM 4 O TYR A 1 0.962 -1.664 -1.607 1.00 0.00
O
ATOM 5 CB TYR A 1 -0.439 0.111 1.007 1.00 0.00
C
ATOM 6 CG TYR A 1 -0.199 1.309 0.109 1.00 0.00
C
ATOM 7 CD1 TYR A 1 1.106 1.803 -0.070 1.00 0.00
C
ATOM 8 CD2 TYR A 1 -1.278 1.943 -0.531 1.00 0.00
C
ATOM 9 CE1 TYR A 1 1.333 2.915 -0.899 1.00 0.00
C
ATOM 10 CE2 TYR A 1 -1.053 3.054 -1.362 1.00 0.00
C
ATOM 11 CZ TYR A 1 0.254 3.540 -1.549 1.00 0.00
C
ATOM 12 OH TYR A 1 0.477 4.617 -2.356 1.00 0.00
O
ATOM 13 H TYR A 1 0.029 -3.037 1.453 1.00 0.00
H
ATOM 14 HA TYR A 1 -1.267 -1.206 -0.312 1.00 0.00
H
ATOM 15 HB2 TYR A 1 -1.419 0.277 1.456 1.00 0.00
H
ATOM 16 HB3 TYR A 1 0.328 0.169 1.780 1.00 0.00
H
ATOM 17 HD1 TYR A 1 1.937 1.327 0.430 1.00 0.00
H
ATOM 18 HD2 TYR A 1 -2.284 1.576 -0.385 1.00 0.00
H
ATOM 19 HE1 TYR A 1 2.336 3.290 -1.038 1.00 0.00
H
ATOM 20 HE2 TYR A 1 -1.883 3.535 -1.857 1.00 0.00
H
ATOM 21 HH TYR A 1 -0.357 4.923 -2.720 1.00 0.00
H
ATOM 22 H TYR A 1 -0.703 -1.863 2.274 1.00 0.00
H
If you take a look at NTYR in xleap:
edit NTYR
and then select Display->Names
You will see that N terminal tyrosine does not have an atom called H. It has
3 hydrogens attached to the peptide N called H1, H2 and H3. Thus Leap is correct and there is a problem with your pdb file in that it is not terminated properly.
Simple solution is to delete the H atom lines (since strangely you have two in your pdb file):
ATOM 13 H TYR A 1 0.029 -3.037 1.453 1.00 0.00
H
...
ATOM 22 H TYR A 1 -0.703 -1.863 2.274 1.00 0.00
H
and let leap add in the 3 missing hydrogens for you. Then all should be good.
Good luck,
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Brothers, Michael Charles
> Sent: Monday, July 06, 2009 6:25 PM
> To: AMBER Mailing List
> Subject: [AMBER] Tleap input error, atom not found in residue template
>
>
> Amber Users,
>
> I am having a strange issue where all but one atom in my pdb file is
> being recognized. I've tried ff99sb and ff03 forcefields so far.
> Upon loading this into tleap, it is adding three hydrogens to places
> there were lone pairs (I'm assuming from adding hydrogens to nitrogen
> lone pairs). It also spits back a message that one atom isn't found
> in the residue template. This is causing an error in the output of
> the prmtop file when I use saveamberparm. I believe this is an issue
> with the carboxy terminus, but I have tried multiple variations and
> have checked other input files and have had little luck.
>
> Any idea how to fix the nomenclature to avoid the error?
>
> Thanks!
>
> Mike
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Received on Tue Jul 07 2009 - 10:09:38 PDT
