Hi Wenjuan,
Sorry for the late reply since I was out of town for a period during the vacation.
The following file would be helpful:
$AMBERHOME/AmberTools/examples/mtkpp/MCPB/CCCC-1A5T/data/1A5T_sidechain.bcl
Best,
Pengfei
On Dec 27, 2014, at 11:26 PM, wjli <wenjuanli93.gmail.com> wrote:
> Dear Amber members,
>
> I have found the same question in mailing list.Sadly,it have no accurate reply about following error:
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB::addFragment ###
> ### Message: Incorrect use ... exiting
> ### ### ### ###
>
> During the addFragment step,I think CYM have no atom forms a ToRsion with the fragment and <atom1> and <atom2> .Thus I added the CH3 group using the following line.
> addFragment terminal/CH3 bd /NAME/CLR/CM1-3/.CB. ag /NAME/CLR/CM1-3/.SG.
>
> But it seems wrong to ignore tr,so what what the correct syntax is?
>
> I look forward to your reply!
> wjli
> _______________________________________________
> 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 Thu Jan 08 2015 - 09:00:03 PST
