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 gromacs...@126.com 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 4.5.1Source code file: toppush.c, line: 1631Fatal 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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