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

[Mark Abraham]

And did you choose "none" for the termini generation? Otherwise when
pdb2gmx tries to combine the default tdb option with your residue, it'll
fail because... drum roll... there's no nitrogen!

Mark


On Sun, Apr 13, 2014 at 2:42 PM, Albert <mailmd2011 at gmail.com> wrote:

>
> 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
>>
>
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