Re: Getting extra atoms by Patching!

From: Michelle Kuttel (mkuttel_at_cs.uct.ac.za)
Date: Sat May 03 2014 - 01:11:50 CDT

Hi Sadegh

Yes, a patch will generate atoms according to the templates in the topology file (in your case ASP, LYS and LINK). If the extra atoms are there in the original residues (ASP and LYS) and are not deleted in your patch, they will remain. The pdb file is used for coordinates, not as the rule/guide for the number of atoms.
regards
-----------------------------
Michelle Kuttel
-----------------------------

On 03 May 2014, at 1:51 AM, Sadegh Faramarzi Ganjabad <safaramarziganjabad_at_mix.wvu.edu> wrote:

> 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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