Atom CA not found in residue

[vijay singh]

I was trying to use amberff03 force field with Gromacs on CUDA. I have renamed the atoms in the pdb file as per the amber standards following the protocol in amberff*.rtp

I get the following error -

Program pdb2gmx, VERSION 4.0.5
Source code file: genhydro.c, line: 304

Fatal error:
Atom CA not found in residue ALA35 while adding hydrogens


The *.rtp file has the following for ALA residue -
[ ALA ]
[ atoms ]
N amber99_34 -0.404773 1
H amber99_17 0.294276 2
CA amber99_11 -0.027733 3
HA amber99_19 0.120802 4
CB amber99_11 -0.229951 5
HB1 amber99_18 0.077428 6
HB2 amber99_18 0.077428 7
HB3 amber99_18 0.077428 8
C amber99_2 0.570224 9
O amber99_41 -0.555129 10



I am not sure where the problem lies.

VJ

[Christopher Bruns]

The error message indicates that residue alanine 35 of your PDB file has no "CA" atom. Is your PDB file perhaps missing an atom?

[vijay singh]

I should have mention that too in my earlier post. Sorry. My pdb files does have the corresponding atoms -

ATOM 262 N ALA 35
aTOM 263 CA ALA 35
ATOM 264 C ALA 35
ATOM 265 O ALA 35

VJ

[Christopher Bruns]

If those records are pasted directly from your PDB file, I think you might need to capitalize the "ATOM" record name for atom CA. That is, "ATOM" instead of "aTOM".

[vijay singh]

Great. Thanks. I have no idea how I could have missed that.

Thanks again,
VJ