On 7/31/12 7:48 AM, Ali Alizadeh wrote:
Dear All usres:
I am trying to do a simple system that contains 4 molecules ethane and
MD run using GROMACS. I build my .pdb file by using Avogadro software
. Afterwards, I try to generate the topology and .gro file using
pdb2gmx program and it generates an error. I am using the 43a1 force
field.
pdb2gmx isn't magic:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
-Justin
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.0
HETATM 1 C LIG 1 -1.328 5.677 -0.487 1.00 0.00 C
HETATM 2 C LIG 1 0.160 5.696 -0.216 1.00 0.00 C
HETATM 3 C LIG 2 -2.612 1.541 -0.437 1.00 0.00 C
HETATM 4 C LIG 2 -1.247 1.959 0.060 1.00 0.00 C
HETATM 5 C LIG 3 -0.924 -2.018 0.494 1.00 0.00 C
HETATM 6 C LIG 3 0.583 -1.901 0.467 1.00 0.00 C
HETATM 7 C LIG 4 0.836 -5.626 -0.170 1.00 0.00 C
HETATM 8 C LIG 4 2.339 -5.464 -0.149 1.00 0.00 C
HETATM 9 H LIG 1 -1.676 6.669 -0.790 1.00 0.00 H
HETATM 10 H LIG 1 -1.878 5.379 0.410 1.00 0.00 H
HETATM 11 H LIG 1 -1.564 4.970 -1.287 1.00 0.00 H
HETATM 12 H LIG 1 0.396 6.406 0.582 1.00 0.00 H
HETATM 13 H LIG 1 0.710 5.990 -1.115 1.00 0.00 H
HETATM 14 H LIG 1 0.508 4.705 0.091 1.00 0.00 H
HETATM 15 H LIG 2 -3.153 2.402 -0.840 1.00 0.00 H
HETATM 16 H LIG 2 -3.203 1.113 0.378 1.00 0.00 H
HETATM 17 H LIG 2 -2.520 0.790 -1.227 1.00 0.00 H
HETATM 18 H LIG 2 -0.651 2.374 -0.758 1.00 0.00 H
HETATM 19 H LIG 2 -0.709 1.102 0.476 1.00 0.00 H
HETATM 20 H LIG 2 -1.338 2.717 0.843 1.00 0.00 H
HETATM 21 H LIG 3 -1.230 -3.068 0.452 1.00 0.00 H
HETATM 22 H LIG 3 -1.365 -1.498 -0.362 1.00 0.00 H
HETATM 23 H LIG 3 -1.328 -1.578 1.410 1.00 0.00 H
HETATM 24 H LIG 3 0.891 -0.853 0.527 1.00 0.00 H
HETATM 25 H LIG 3 0.984 -2.323 -0.459 1.00 0.00 H
HETATM 26 H LIG 3 1.025 -2.438 1.312 1.00 0.00 H
HETATM 27 H LIG 4 2.612 -4.409 -0.060 1.00 0.00 H
HETATM 28 H LIG 4 2.771 -6.003 0.699 1.00 0.00 H
HETATM 29 H LIG 4 2.781 -5.858 -1.069 1.00 0.00 H
HETATM 30 H LIG 4 0.564 -6.681 -0.264 1.00 0.00 H
HETATM 31 H LIG 4 0.394 -5.238 0.753 1.00 0.00 H
HETATM 32 H LIG 4 0.402 -5.082 -1.015 1.00 0.00 H
END
FATAL ERROR: Residue "LIG" not found in residue topology database.
Sincerely
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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