[gmx-users] No default U-B types in CHARMM36 FF

[Albert]

Hello Mark:

thanks a lot for kind comments. I add ACE and NMA in the N-ter and C-ter 
at the protein respectively and I run command:

pdb2gmx -f p.pdb -o gmx.pdb

but failed with messages:

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.5
Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line: 
1148

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Here is my ACE and NMA coordinate in input .pdb file:

ATOM      1  C   ACE X  35       9.430  28.580  76.350  0.00 
0.00           C
ATOM      2  O   ACE X  35       9.590  28.680  75.140  0.00 
0.00           O
ATOM      3  CH3 ACE X  35       8.670  29.670  77.110  0.00 
0.00           C

ATOM   2363  N   NMA X 339      51.520  10.650  31.420  0.00 
0.00           N
ATOM   2364  CH3 NMA X 339      51.540   9.620  30.390  0.00 
0.00           C


I don't know why it claimed above errors...

thank you very much.

ALbert



On 04/13/2014 12:39 PM, Mark Abraham wrote:
> Hi,
>
> Looks like nobody has parametrized that interaction. Not too surprising,
> though, since you won't often get NH2 in water at biological pH!
>
> Mark