Check the topology section in the gromacs manual.
You'll find the format you should use for bonds, angles etc.
On 15-02-11, gromacs564 <[email protected]> wrote:
Dear All:I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter.I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate:-------------------------------------------------------
Program grompp_m, VERSION 4.5.1
Source code file: toppush.c, line: 1631
Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.
For more information and tips for troubleshooting, please check the GROM···
--------------------------------------------------------------------------------------------I added some bonds and angles parameters like this:······························
; residue 44 ASN rtp ASN q 0.0
664 N 44 ASN N 664 -0.430106 14.01 ; qtot 4.57
665 HD 44 ASN HD 665 0.250466 2.016 ; qtot 4.824
666 CT 44 ASN CA 666 0.044609 12.01 ; qtot 4.869
···············
[ bonds ]
; ai aj funct c0 c1 c2 c3
···
676 678 1
678 679 1 0.10115
678 680 1
680 681 1
·······················
[ angles ]
; ai aj ak funct c0 c1 c2 c3
························
648 650 652 1
651 650 652 1 115.149
650 652 653 1
650 652 654 1
····················Any help will highly appreciated!
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