[gmx-users] How to simulate peptide capped with ACE?

[Mark Abraham]

fufengliu at tju.edu.cn wrote:
> Dear gromacs users,
> I trying to simulate a peptide capped with ACE, when I run grompp, I got the
> following error:
> WARNING 1 [file "1.top", line 306]:
>   No default G96Angle types, using zeroes.
> I checked the topology and found the ACE group disappears. I think that the grompp
> doesn¡¯t handle correctly the ACE group. I had browsed to the mailing list archive
> and found lots of problems similar to mine, but I couldn¡¯t know how to solve it?
> Someone can tell me in detail how to do it? 

No, because you haven't told us what you're trying to do - even what 
force field you're trying to use. If you're using pdb2gmx, you need to 
name the residue in the initial structure in a way that allows it to 
recognise it as ACE, so read ffxxxx.rtp and see what acetyl caps get 
called for force field xxxx. Or, read chapter five of the manual and 
learn how this stuff works!!

Mark