[gmx-users] Incorrect bond in top file

[Shima Arasteh]

Dear users,


[ Especially dear Justin ( please don't shout at me! ) ],


As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp of the force field ( CHARMM36). The first step is "generating top file". When I ran the command of pdb2gmx, the top file is generated, but it contains a bond which I have not defined in the FVAL. The incorrect bond is between H-atom of valine (  this H is one of the atoms connected to the N of valine and this N is in the backbone, The N of valine is connected to C of formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of formyl doesn't form a second ordered bond with O ).

aminoacids.hdb and aminoacids.rtp are the files I modified. 


Do you have any suggestions? Please help me. Thanks in advance.
Sincerely,
Shima