Dear GROMACS gremlins,
I am trying in vain to implement the GoIP parameters for a gold-peptide
interface in the OPLSAA ff. I began with just one kind of Au atom and
now I want to put in two.
When I execute gmx grompp -f em.mdp -c Au111.gro -p topol.top -o em.tpr
I get this error
Fatal error:
Something is wrong in the coordinate formatting of file Au111.gro. Note
that gro is fixed format (see the manual)
For more information and tips for troubleshooting, please check the
GROMACS
Here is my .gro file
New structure; 1Created by VESTA
4
1AU AUI 1 0.000 0.000 0.240
1AU AUS 2 0.022 1.282 0.240
1AU AUI 3 0.045 2.564 0.240
1AU AUS 4 1.929 0.000 0.240
0.00000 0.00000 0.00000
And my .top file:
; Include forcefield parameters
#include "./oplsaa_Au.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Other 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 AU rtp AU q 0.0
1 opls_966 1 AU AUI 1 0.0 79 ;
qtot 0
2 opls_967 1 AU AUS 2 -0.3 79 ;
qtot 0
3 opls_966 1 AU AUI 3 0.0 79 ;
qtot 0
4 opls_967 1 AU AUS 4 -0.3 79 ;
qtot 0
;Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
;Name
New structure; 1Created by VESTA
[ molecules ]
;Compound #mols
Other 1
And the ffnonbonded.itp:
opls_966 AUI 79 196.96657 0.0 A 3.20000e-01
6.50000e-01
opls_967 AUS 79 196.96657 -0.3 A 0.00000e-01
0.00000e-01
opls_968 AUB1 79 196.96657 0.0 A 0.00000e-01
0.00000e-01
opls_969 AUB2 79 196.96657 0.3 A 0.00000e-01
0.00000e-01
(there are extra Au atoms as I will eventually be adding more kinds)
I also changed the residuetype.dat file to include:
AUI Ion
AUS Ion
I can't see where I've gone wrong as I read that grompp does not read
the .rtp file or .atp. Also can you explain to me what is the difference
between atom_type (eg opls_XXXX) and atom (eg AUI).
Thanks for your help
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