Fellow gmx users,
I made a tolopgy file for TFE in water by "hand" for the OPLSAA/L force field to be used in a simulation containing a mixed solvent. I made a similar TFE.itp file and included it in the mixed solvent topology file. when I ran grompp before equilibrating the system I received an error message that read:
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448
Fatal error:
number of coordinates in coordinate file (tfe.gro, 9)
does not match topology (tfe_mike.top, 0)
-------------------------------------------------------
Do you know why my topology file contains zero coordinates? My topology file is pasted below:
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
TFE 3
[ atoms ]
; nr type resnr residue atom cgnr charge
1 opls_161 1 TFE C1 1 0.797
2 opls_164 1 TFE F2 1 -0.285
3 opls_164 1 TFE F3 1 -0.280
4 opls_164 1 TFE F4 1 -0.278
5 opls_160 1 TFE C5 2 -0.033
6 opls_162 1 TFE O6 3 -0.479
7 opls_163 1 TFE H7 3 0.292
8 opls_165 1 TFE H8 2 0.133
9 opls_165 1 TFE H9 2 0.132
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.13570 351456.0
1 3 1 0.13570 351456.0
1 4 1 0.13570 351456.0
1 5 1 0.15100 292880.0
5 6 1 0.13640 376560.0
6 7 1 0.09450 462750.4
5 8 1 0.10900 284512.0
5 9 1 0.10900 284512.0
[ pairs ]
[ angles ]
; ai aj ak funct c0 c1
2 1 5 1 109.5 418.4
3 1 5 1 109.5 418.4
4 1 5 1 109.5 418.4
1 5 8 1 110.7 313.8
1 5 6 1 109.5 418.4
1 5 9 1 110.7 313.8
5 6 7 1 108.5 460.24
8 5 9 1 107.8 276.144
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 3 1.12968 3.38904 0.00000 -4.51872 0.0000 0.0000
3 1 5 6 3 1.12968 3.38904 0.00000 -4.51872 0.0000 0.0000
4 1 5 6 3 1.12968 3.38904 0.00000 -4.51872 0.0000 0.0000
1 5 6 7 3 0.26778 -9.36798 9.10020 0.00000 0.0000 0.0000
2 1 5 8 3 0.65689 1.97066 0.00000 -2.62755 0.0000 0.0000
3 1 5 8 3 0.65689 1.97066 0.00000 -2.62755 0.0000 0.0000
4 1 5 8 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000
2 1 5 9 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000
3 1 5 9 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000
4 1 5 9 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000
[ dihedrals ]
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "tip4p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include generic topology for ions
#include "ions.itp"
#include "tfe_mike.itp"
[ system ]
30% TFE in water
[ molecules ]
; Compound #mols
TFE 14
SOL 128
Thanks in advance for your assistance,
Michael Owen
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