Getting extra atoms by Patching!

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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