On 30/07/2012 7:41 PM, Shima Arasteh wrote:
You are right, CT1 is incorrect for sure. But the other option is C(carbonyl
C) . Maybe I couldn't say it clearly.
The FVAL which I sent before through mailing list, is the result of this
formamide and the CGenff generation:
[ FVAL ]
[ atoms ]
CN C 0.357 0
ON O -0.51 1
H1 HA 0.100 2
N NH1 -0.423 3
HN H 0.333 4
CA CT1 0.034 5
HA HB 0.09 6
CB CT1 -0.093 7
HB HA 0.09 8
CG1 CT3 -0.268 9
HG11 HA 0.09 10
HG12 HA 0.09 11
HG13 HA 0.09 12
CG2 CT3 -0.268 13
HG21 HA 0.09 14
HG22 HA 0.09 15
HG23 HA 0.09 16
C C 0.528 17
O O -0.510 18
[ bonds ]
CN H1
CN ON
CN N
N H
CA N
CA HA
CA C
C O
CA CB
CB HB
CB CG1
CB CG2
CG2 HG21
CG2 HG22
CG2 HG23
CG1 HG11
CG1 HG12
CG1 HG13
[ impropers ]
CN N ON H1
This is the new residue which I defined and sent you(as remember), I used these
parameters and atomtypes , and then went through mailing list and asked for
your help a few days ago.
All over , with this procedure , I couldn't get the an acceptable result.
You say you've chosen suitable atom types. grompp says it can't find
parameters for interactions using them. So until you find out further
information, you don't have suitable atom types. I've said all I have
to say until you go and look up whether the bonds, angles and dihedrals
that you want to use are defined in your force field for the atom types
you want to use.
If you want further help, you will need to paste your .rtp entry(s), the
N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full
pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp
command line, and full grompp output. You may think your context is
clear, but nobody else is paying your problem as much attention as you
are. I won't help further if you only provide partial information.
Mark
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