Hi all,
I would like to run a simulation in amber using amoeba. I have been able to
generate the parameters for the protein but I have some after having made a
periodic box with counter ions - in my case it is chloride ions. I am not
able to generate a reasonable xyz from tinker. Below is the output from
tinker from a pdbfile :
5796
1 N -0.104000 -6.979000 -1.437000 0 2 3 4
5
2 H1 -1.104000 -6.887000 -1.333000 0 1
3 H2 0.229000 -7.666000 -0.776000 0 1
4 H3 0.113000 -7.076000 -2.419000 0 1
5 CA 0.512000 -5.722000 -1.029000 0 1 6 7
11
when the chord ion is present it is able to generate the correct xyz where
atoms are present:
1 N -2.105975 -5.638585 2.673563 231 2 5 6 7
2 CA -1.957000 -4.255499 2.239845 8 1 3 8
9
3 C -2.805890 -3.337413 3.105317 9 2 4 13
4 O -3.913220 -3.705420 3.491259 11 3
5 H -1.738125 -5.717874 3.618823 232 1
6 H -1.547836 -6.274138 2.118100 232 1
Here the right atom types are added when I look into the parameter file - I
have amoebapro13 and ambertools14. My question is why this goes wrong with
the chloride ion present - I have tried different naming schemes and
placements of the residue name or atom name but same problem. So it seems
that it is able to recognize it
135 CL -6.321000 4.872000 -5.386000 0
should I put it together piece by piece? Any help or suggestions would be
highly appreciated thanks
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Received on Sat Sep 13 2014 - 22:00:02 PDT
