Hi,
I have just started to learn gromacs. I am facing a problem to make topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
-------------------------------------------------------
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N atom with
should be linked with ACE, but my conf.pdb files does not have any. I have
topol.top file from the tutorial but didn't show how I can generate that.
I am a totally newbie, thus I am wondering what should I do. Which file I
should correct to get rid of those? Do I need to know the bonding of every atom
in the molecule for that?
Thanks in advance
Tawhid
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