Never mind, I see that none of the standard library files have C terminal
CYM resides defined so that's the source of the error. Not sure why, maybe
when someone added them long ago they didn't set up the terminal versions.
It would take a bit of work to build them from scratch.
The ipq protein force fields have these CCYM definitions though, but that's
a larger change. You can look into it and see if that's a good option for
you.
Carlos
On Sat, Aug 2, 2025, 5:54 PM Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> I'm traveling right now so can get back to you later with details, but
> Dave is right thslat ff19sb does not include special treatment for terminal
> residues lacking either a phi or psi. But I will check on how to load a
> library that will get rid of the error.
>
>
> On Sat, Aug 2, 2025, 5:09 PM David A Case via AMBER <amber.ambermd.org>
> wrote:
>
>> On Fri, Aug 01, 2025, Simona Saporiti via AMBER wrote:
>>
>> >I am performing a simulation using ff19SB force field.
>> >When using tleap a fatal error occurs about the atom OXT of CYM.
>> >After some testing I figured out that CCYM (CYM C-terminal) is not
>> available for both ff19SB and ff14Sb (I didn't test any other ff).
>> >Do you know if parameters for CCYM exist anywhere?
>>
>> The Stony Brook people can answer better than I can, but here is what is
>> probably a good start: look at the differences between CYM and CYX in the
>> amino19.lib file in the dat/leap/lib folder. Then try to use those same
>> differences to convert CCYX to CCYM in aminoct12.lib.
>>
>> You don't have to worry about CMAP terms, since (I hope I am correct
>> here!)
>> ff19SB doesn't use CMAP for the N- and C-terminal residues.
>>
>> Better answers may be forthcoming soon on the this list.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 03 2025 - 14:00:03 PDT
