Subject: Re: Subject: Re: Subject: Re:Re: New partial charges after patching

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Tue Jul 22 2014 - 05:04:09 CDT

• Next message: George Patargias: "Cost of a colvar calculation"
• Previous message: Jérôme Hénin: "Re: Inquiry about forceConstant"
• Next in thread: Kenno Vanommeslaeghe: "2-residue patch for Asn-Lys side chain amide bond"
• Reply: Kenno Vanommeslaeghe: "2-residue patch for Asn-Lys side chain amide bond"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Kenno

Following is the patch;

PRES LINK 0.00 ! linkage for IMAGES or for joining segments
                                  ! 1 refers to previous (N terminal) -->
Asp3
                                  ! 2 refers to next (C terminal) --> Lys10
                                  ! use in a patch statement
                                  ! follow with AUTOgenerate ANGLes
DIHEdrals command
   ! used to link Asp3 to Lys10 in shu-9119
   !
   ! 1HB1 1HB2
   ! \ /
   ! --1CB
   ! \
   ! 1CG==OD1
   ! \
   ! 2NZ- 2HZ1
   ! |
   ! 2HE2 - 2CE- 2HE1
   ! |

DELETE ATOM 1OD2
DELETE ATOM 2HZ2
DELETE ATOM 2HZ3
!GROUP
!ATOM CB CT2A -0.27
!ATOM HB1 HA2 0.10
!ATOM HB2 HA2 0.10
!ATOM CG CC 0.63
!ATOM OD1 OC -0.75
!ATOM CE CT2 0.22
!ATOM HE1 HA2 0.06
!ATOM HE2 HA2 0.06
!ATOM NZ NH3 -0.29
!ATOM HZ1 HC 0.34

BOND 1CG 2NZ

Sadegh

• Next message: George Patargias: "Cost of a colvar calculation"
• Previous message: Jérôme Hénin: "Re: Inquiry about forceConstant"
• Next in thread: Kenno Vanommeslaeghe: "2-residue patch for Asn-Lys side chain amide bond"
• Reply: Kenno Vanommeslaeghe: "2-residue patch for Asn-Lys side chain amide bond"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:37 CST