From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Fri May 02 2014 - 18:51:31 CDT
Hello
I use patch to link ASP to LYS. However, after generating psf and pdb files
I see 5 extra new atoms in the center of coordinate which belong to ASP
residue, but in fact they don't belong to it in original pdb file. Has
anybody faced with such a problem before?
Thank you in advance
Sadegh
Following is what I put in topology file;
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
!
! 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
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