[gmx-users] (no subject)
Patel Ronak Y
ronakp at iitb.ac.in
Tue Apr 27 17:47:00 CEST 2004
Hi all,
I am simulating six heptapeptides as a different chains in water. The N
terminus has -CO-CH3 and the C-terminus has NH-CH3.The simulation works
well but when I use xrama and g_rama to check dihedral angles. I get the
following error.
Dihedral X, Y not found in topology. (X,Y are the numbers of O of -CO of
7th residue and Y is the number of H of NAC as mention in the .top file
created by pdb2gmx)
Everything works nicely with one heptapeptide.
These are my topology of extra groups that I have introduced in the
ffG43a1.rtp.
[ ACE ]
[ atoms ]
CA CH3 0.000 0
C C 0.380 1
O O -0.380 1
[ bonds ]
C CA gb_26
C O gb_4
C +N gb_9
[ angles ]
CA C +N ga_18
O C +N ga_32
CA C O ga_29
[ impropers ]
C CA +N O gi_1
[ dihedrals ]
CA C +N +CA gd_4
[ NAC ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA CH3 0.000 1
[ bonds ]
N H gb_2
N CA gb_20
[ angles ]
-C N H ga_31
H N CA ga_17
-C N CA ga_21
[ impropers ]
N -C CA H gi_1
[ dihedrals ]
-CA -C N CA gd_4
Can somebody plz tell me where is the error.
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