[gmx-users] gro to itp file
Justin Lemkul
jalemkul at vt.edu
Tue Oct 30 02:16:12 CET 2018
On 10/26/18 10:13 AM, Anubha Agrawal wrote:
> Hello gmx users,
>
> Please ignore my previous post. My query is following-
>
> I've prepared a coordinate file in .gro format using pdb2gmx. I obtained
> the pdb from openbabel online server and used it for pdb2gmx command.
> Further, I've identified CHARMM36 atom types for my molecule. This molecule
> is one of the model compounds for lignin. I've included the new residue
> information of the molecule in .rtp file. Now I want to generate a GROMACS
> topology file for the same. Any help will be appreciated.
>
> The .gro file is:
>
> 43
>
> 1LIG O 1 0.300 0.000 0.000
>
> 1LIG O 2 0.387 -0.050 0.000
>
> 1LIG O 3 0.500 0.173 0.000
>
> 1LIG O 4 0.783 0.037 0.000
>
> 1LIG O 5 0.200 -0.173 0.000
>
> 1LIG O 6 0.783 -0.163 0.000
>
> 1LIG C 7 0.350 0.087 0.000
>
> 1LIG C 8 0.437 0.037 0.000
>
> 1LIG C 9 0.523 -0.013 0.000
>
> 1LIG C 10 0.400 0.173 0.000
>
> 1LIG C 11 0.610 0.037 0.000
>
> 1LIG C 12 0.523 -0.113 0.000
>
> 1LIG C 13 0.200 0.000 0.000
>
> 1LIG C 14 0.696 -0.013 0.000
>
> 1LIG C 15 0.610 -0.163 0.000
>
> 1LIG C 16 0.696 -0.113 0.000
>
> 1LIG C 17 0.150 -0.087 0.000
>
> 1LIG C 18 0.150 0.087 0.000
>
> 1LIG C 19 0.050 -0.087 0.000
>
> 1LIG C 20 0.050 0.087 0.000
>
> 1LIG C 21 0.000 0.000 0.000
>
> 1LIG C 22 0.870 -0.013 0.000
>
> 1LIG C 23 0.300 -0.173 0.000
>
> 1LIG H 24 0.263 0.137 0.000
>
> 1LIG H 25 0.487 0.123 0.000
>
> 1LIG H 26 0.400 0.273 0.000
>
> 1LIG H 27 0.313 0.223 0.000
>
> 1LIG H 28 0.610 0.137 0.000
>
> 1LIG H 29 0.437 -0.163 0.000
>
> 1LIG H 30 0.287 -0.050 0.000
>
> 1LIG H 31 0.610 -0.263 0.000
>
> 1LIG H 32 0.200 0.173 0.000
>
> 1LIG H 33 0.550 0.260 0.000
>
> 1LIG H 34 0.000 -0.173 0.000
>
> 1LIG H 35 -0.000 0.173 0.000
>
> 1LIG H 36 -0.100 -0.000 0.000
>
> 1LIG H 37 0.783 -0.263 0.000
>
> 1LIG H 38 0.970 -0.013 0.000
>
> 1LIG H 39 0.920 0.073 0.000
>
> 1LIG H 40 0.870 -0.113 0.000
>
> 1LIG H 41 0.387 -0.223 0.000
>
> 1LIG H 42 0.300 -0.273 0.000
>
> 1LIG H 43 0.350 -0.087 0.000
>
> 0.00000 0.00000 0.00000
You have non-unique atom names, which will not be interpreted correctly
by pdb2gmx.
>
> Residue information used in .rtp file is-
>
> [ LIG ]
> [ atoms ]
> HP HP1 0.115
> CA CA1 -0.115
> CA CA2 -0.115
> HP HP2 0.115
> CA CA3 -0.115
> HP HP3 0.115
> CA CA4 0.22
> OC30A OC30A1 -0.39
> CT3 CT32 -0.1
> HA HA07 0.09
> HA HA08 0.09
> HA HA09 0.09
> CA CA5 0.22
> CA CA6 -0.115
> HP HP6 0.115
> OC30A OC30A2 -0.39
> CT1 CT11 0.22
> CT2 CT21 0.05
> HA HA00 0.09
> HA HA01 0.09
> OH1 OH11 -0.65
> H H1 0.42
> HA HA02 0.09
> CT1 CT12 0.14
> OH1 OH12 -0.65
> HA HA03 0.09
> H H2 0.42
> CA CA7 0.000
> CA CA8 -0.115
> CA CA9 -0.115
> HP HP8 0.115
> HP HP9 0.115
> CA CA10 0.11
> OH1 OH13 -0.54
> H H3 0.43
> CA CA11 0.22
> OC30A OC3AO3 -0.39
> CT3 CT31 -0.1
> HA HA04 0.09
> HA HA05 0.09
> HA HA06 0.09
> CA CA12 -0.115
> HP HP12 0.115
You have inverted the atom name and type fields, and you have omitted
the charge group column. This entry will be non-functional.
-Justin
> [ BONDS ]
> CA1 HP1
> CA1 CA2
> CA2 HP2
> CA2 CA3
> CA3 HP3
> CA3 CA4
> CA4 CA5
> CA5 CA6
> CA6 CA1
> CA6 HP6
> CA5 OC30A2
> CA4 OC30A1
> OC30A1 CT32
> CT32 HA07
> CT32 HA08
> CT32 HA09
> OC30A2 CT11
> CT11 CT21
> CT21 HA00
> CT21 HA01
> CT21 OH11
> OH11 H1
> CT11 HA02
> CT22 CT12
> CT12 OH12
> CT12 HA03
> CT12 CA7
> CA7 CA8
> CA8 HP8
> CA8 CA9
> CA9 HP9
> CA9 CA10
> CA10 CA11
> CA11 CA12
> CA12 CA7
> CA12 HP12
> CA11 OC30A3
> OC30A3 CT31
> CT31 HA04
> CT31 HA05
> CT31 HA06
> CA10 OH13
> OH13 H3
> OH12 H2
>
> Thanks
>
> Regards’
>
> Anubha
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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