You include unk.itp but show us drg.itp. Perhaps you're looking at or
using the wrong file.
/Erik
qing yang skrev:
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from
prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs.
But when I issue a grompp command for minimization,grompp gives a
fatal error.
The error is:
Error 0 [file "unk.itp",line 4]
Not enough parameters
…..
Fatal error:
Bonded/nonbonded atom type '1' not found!
My pro.top file:
#include “ffg43a1.itp”
#include “unk.itp”
[molecules]
Protein 1
UNK 1
SOL 109324
My drg.itp file:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR1 1 UNK CBF 1 0.003 12.0110
2 HC 1 UNK HBF 1 0.035 1.0080
...............
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.109 12300000.0 0.109 12300000.0 ; CBF HBF
1 3 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBG
.............
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; CBF NBK
1 9 1 ; CBF CBI
.................
[ angles ]
; ai aj ak fu c0, c1, ...
2 1 3 2 120.0 505.0 120.0 505.0 ; HBF CBF CBG
2 1 13 2 120.0 505.0 120.0 505.0 ; HBF CBF CBE
................
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 13 3 2 2 0.0 167.4 0.0 167.4 ; imp CBF CBE CBG HBF
3 1 5 4 2 0.0 167.4 0.0 167.4 ; imp CBG CBF CBH HBG
Maybe someone knows what the problem might be?How can I deal with this
problem?
Thanks for your help!
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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