[gmx-users] alamethicin error

[Mark Abraham]

pragya chohan wrote:
> Thanks Mark. The C terminal does not have a -COOH group at the end but rater has a -OH group.... PHL is actually PHENYLALANINOL.
> But when i put option 2 whn prompted for 
> select C-terminus type (end)>> 0: COO->> 1: COOH>> 2: None 

Well that won't give you phenylalaninol as a C-terminal fragment.

>  i still get an error Atom C not found in residue 21 while adding improper.
> I checked the naming in ffgmx.rtp but everything seems to be fine. 

There's no atom named C in PHL, so it can't be fine. If phenylalaninol 
doesn't have a -CO- fragment to link to the next residue, then this 
problem will occur. The carbonyl carbon is conventionally named "C" and 
the next residue expects to be able to make an amide bond to it with its 
amino N. I don't know what the chemistry for your structure is, but if 
it doesn't involve normal peptide linkages between residues then pdb2gmx 
will struggle. You may need to look up specbond.dat in the manual/wiki.

Mark