[gmx-users] multichain peptide simulation
Susan Idiula
susan19 at iitb.ac.in
Wed May 5 12:20:01 CEST 2004
Hi,
I am simulating six heptapeptides (as different chains) in water. Each
peptide has the N terminus as -CO-CH3 and the C-terminus as NH-CH3.The
simulation works well but when I use xrama and g_rama to check dihedral
angles. I get the following error:
Fatal error: Dihedral X, Y not found in topology. (X,Y are the atom
numbers of O of -CO of 7th residue and Y is the atom number of H of NAC as
mentioned in the .top file created by pdb2gmx)
Everything works nicely with one heptapeptide.
These are the topology of the 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
I have 7 residues per chain, so in principle I should be getting 7x6 =42
phi-psi combinations, but xrama calculates 47 phi-psi combinations. i
presume it has to do something with the ends of each chain, but i am not
sure.
i have tried removing the extra CO-CH3 AND NH-CH3, but it didnot work.
any suggestions?
thanx
susan
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