[gmx-users] Including and itp file, for a residue

[Arneh Babakhani]

Hi, thank you for your input. I did that. Now I'm getting this error.

-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toputil.c, line: 61

Fatal error:
Atomtype 'CA' not found!
-------------------------------------------------------


This doesn't make much sense, since in the dmpc.itp file, the 5th atom 
of the DMPC residue has the name 'CA'.

Here's an excerpt from my pdb file. Any thoughts???

CRYST1 61.760 61.760 66.608 90.00 90.00 90.00 P 1 1
ATOM 1 CA DMPC 1 11.243 45.515 16.151 1.00 0.00
ATOM 2 CB DMPC 1 13.362 44.484 16.520 1.00 0.00
ATOM 3 CC DMPC 1 12.191 45.542 18.330 1.00 0.00
ATOM 4 NTM DMPC 1 12.503 45.614 16.897 1.00 0.00

chris.neale at utoronto.ca wrote:
> place it in your .top file.
>
> You can make it yourself. Make a file like this: (change the number of mols at
> the bottom to reflect what you really have).
>
> If you get a message like "double define statement" then try removing the
> lipids.itp include. If you want to add a protein, make a .itp for your protein
> and include that in the top file too. Make sure the order DMPC then SOL (or vice
> versa) is the same between the .top file and the .gro file
>
> ; Include forcefield parameters
> #include "ffG43a2x.itp"
> ; Include topologies
> #include "lipid.itp"
> #include "dmpc.itp"
> #include "spc.itp"
> [ system ]
> ; Name
> [ molecules ]
> ; Compound        #mols
> DMPC              340
> SOL              6729
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