[gmx-users] question
Diogo Vila Viçosa
diogo.vicosa at fc.ul.pt
Wed May 13 10:53:53 CEST 2015
I am not sure but probably you only need to change the residue names in the
pdb file. You should also be carefull with other bonded parameters (angles
and dihedrals).
Em qua, 13 de mai de 2015 às 04:56, Andrew Bostick <
andrew.bostick1 at gmail.com> escreveu:
> Dear Justin
>
> Since I want to consider the special bond between CD atom of GLU residue
> form peptide 1 and NZ atom of LYS residue from peptide 2, I did following
> steps:
>
> 1) I created 1 pdb file containing 2 peptides without any connection
> between aformentioned atoms (CD & NZ). I deleted OE2 atom of GLU residue
> and HZ2 and HZ3 atoms of LYS residue.
>
> 2) I created a new entry in specbond.dat and two .rtp entries in gromos
> 43a1.ff. These are as follows:
>
> In specbond.dat file:
> GLU CD 1 LYS NZ 1 0.13 GLU2 LYS2
>
> In aminoacids.rtp file:
> [ LYS2 ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 1
> CG CH2 0.00000 2
> CD CH2 0.00000 2
> CE CH2 0.00000 3
> NZ NT -0.50000 3
> HZ1 H 0.50000 3
> C C 0.380 4
> O O -0.380 4
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB CG gb_26
> CG CD gb_26
> CD CE gb_26
> CE NZ gb_20
> NZ HZ1 gb_2
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB CG ga_14
> CB CG CD ga_14
> CG CD CE ga_14
> CD CE NZ ga_14
> CE NZ HZ1 ga_10
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB CG gd_17
> CA CB CG CD gd_17
> CB CG CD CE gd_17
> CG CD CE NZ gd_17
> CD CE NZ HZ1 gd_14
> ----------------------------------------------
>
> [ GLU2 ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 1
> CG CH2 0.00000 1
> CD C 0.50000 2
> OE1 OM -0.50000 2
> C C 0.380 3
> O O -0.380 3
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB CG gb_26
> CG CD gb_26
> CD OE1 gb_5
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB CG ga_14
> CB CG CD ga_14
> CG CD OE1 ga_21
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB CG gd_17
> CA CB CG CD gd_17
>
> After using pdb2gmx, I encountered with:
>
> WARNING: atom OE2 is missing in residue Glu 417 in the pdb file.
>
> What is wrong in my steps?
>
> Thanks in advance.
> --
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