AMBER Archive (2009)

Subject: Re: [AMBER] Disappearing common atoms in Amber 10 with TI

• Previous message: Hlengisizwe Ndlovu: "[AMBER] Steered MD.....SHAKE error!!"
• In reply to: Khavrutskii, Ilja: "Re: [AMBER] Disappearing common atoms in Amber 10 with TI"
• Next in thread: case: "Re: [AMBER] Disappearing common atoms in Amber 10 with TI"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi,

> I want the vc-vh bonds that are c-h bonds to be SHAKEn, do I need to wory
> about make that explicit to Amber or would it understand given the Masses
> of the atoms?

I would explicitly make them C-dummy and H-dummys, CD and HD, but you can
quickly check if they are shaken by testing if the bonds appear in the
bonds_with_hydrogen section of the prmtop file...

Regards,

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

• Previous message: Hlengisizwe Ndlovu: "[AMBER] Steered MD.....SHAKE error!!"
• In reply to: Khavrutskii, Ilja: "Re: [AMBER] Disappearing common atoms in Amber 10 with TI"
• Next in thread: case: "Re: [AMBER] Disappearing common atoms in Amber 10 with TI"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]