[gmx-users] make a new bond in VERSION 4.5.4

[Justin A. Lemkul]

Yulian Gavrilov wrote:
> Dear Justin, gmx users,
> 
> I forgot to write, but I added these new residues to aminoacids.rtp.
> 
> Maybe I need to add them also to aminoacids.r2b? How to do it correctly? 

An .r2b entry is unnecessary in this case; these files are only used to 
standardize force field-specific names for certain residues.

> Just new lines in it or add them to lines of Gly and Lys? So, I suppose 
> it is all steps in 
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> 

These should be all the necessary steps.

-Justin

> 
> [ LYQ ]
> 
> [ atoms ]
> 
> N N -0.41570 1
> 
> H H 0.27190 2
> 
> CA CT -0.07206 3
> 
> HA H1 0.09940 4
> 
> CB CT -0.04845 5
> 
> HB1 HC 0.03400 6
> 
> HB2 HC 0.03400 7
> 
> CG CT 0.06612 8
> 
> HG1 HC 0.01041 9
> 
> HG2 HC 0.01041 10
> 
> CD CT -0.03768 11
> 
> HD1 HC 0.01155 12
> 
> HD2 HC 0.01155 13
> 
> CE CT 0.32604 14
> 
> HE1 HP -0.03358 15
> 
> HE2 HP -0.03358 16
> 
> NZ N -0.64977 17
> 
> HZ1 H 0.38604 18
> 
> C C 0.59730 19
> 
> O O -0.56790 20
> 
> [ bonds ]
> 
> N H
> 
> N CA
> 
> CA HA
> 
> CA CB
> 
> CA C
> 
> CB HB1
> 
> CB HB2
> 
> CB CG
> 
> CG HG1
> 
> CG HG2
> 
> CG CD
> 
> CD HD1
> 
> CD HD2
> 
> CD CE
> 
> CE HE1
> 
> CE HE2
> 
> CE NZ
> 
> NZ HZ1
> 
> C O
> 
> -C N
> 
> [ impropers ]
> 
> -C CA N H
> 
> CA +N C O
> 
> 
> 
> [ GLQ ]
> 
> [ atoms ]
> 
> N N -0.41570 1
> 
> H H 0.27190 2
> 
> CA CT -0.02520 3
> 
> HA1 H1 0.06980 4
> 
> HA2 H1 0.06980 5
> 
> C C 0.59730 6
> 
> O O -0.56790 7
> 
> [ bonds ]
> 
> N H
> 
> N CA
> 
> CA HA1
> 
> CA HA2
> 
> CA C
> 
> C O
> 
> -C N
> 
> [ impropers ]
> 
> -C CA N H
> 
> CA +N C O
> 
> 
> -- 
> 
> Sincerely,
> 
> Yulian Gavrilov
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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