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

[chris.neale at utoronto.ca]

CA is not a lipid type. look at dmpc.itp

[ atoms ]
;     id   atype   resnr resname   aname    cgnr  charge    mass
       1     LC3       1   DMPC      CN1       0  0.4000 15.0350
       2     LC3       1   DMPC      CN2       0  0.4000 15.0350
       3     LC3       1   DMPC      CN3       0  0.4000 15.0350
       4     LNL       1   DMPC      NTM       0 -0.5000 14.0067
       5     LH2       1   DMPC       CA       0  0.3000 14.0270
       6     LC2       1   DMPC       CB       1  0.4000 14.0270
etc...

You should have atom names CN1, CN2, CN3 in place of CA, CB, CC



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Previous message was:

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