วันเวลา อมรนพ wrote:
Dear gmx users
I want to simulate propane molecule and I use PRODGE website to generate
both .gro and .top file.
Then I run the grompp program and there is an error said that
Fatal error:
Invalid order for directive moleculetype, file ""topol.top"", line 17
and below is my topology file of a propane molecule
You must #include the appropriate force field file before you can define your
molecule type.
A few notes and suggestions:
1. If using the original PRODRG server, consider using the newer PRODRG 2.5
server. The original PRODRG gives ffgmx-compatible topologies. This force
field is deprecated. PRODRG 2.5 is compatible with the newer Gromos96 variants.
2. Check the charges and charge groups carefully, and consider changing them.
Does it make sense to have permanent dipoles in a propane molecule?
-Justin
;
;
; This file was generated by PRODRG version 071121.0636
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to d...@davapc1.bioch.dundee.ac.uk
<mailto:d...@davapc1.bioch.dundee.ac.uk>
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 -0.007 15.0350
2 CH2 1 DRG CAB 1 0.015 14.0270
3 CH3 1 DRG CAC 1 -0.008 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAA CAB
2 3 1 0.153 334720.0 0.153 334720.0 ; CAB CAC
[ pairs ]
; ai aj fu c0, c1, ...
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 111.0 460.2 111.0 460.2 ; CAA CAB
CAC
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
Please help me figure out what is the error
Thanks for advance
Suwit
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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