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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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