Dear Jorgen, as for my experience with ionic liquids, I have managed to mix
ction and anion parameters in a single tinker "key" file, pay attention to
use different residue numbers. With proteins it should be all much easier,
because you don't have to calculate the parameters with poltype. In any
case, follow the amoeba documentation and contact the authors in case of
problems, they are very kind and always willing to help.
Regards
Lorenzo G.
2014-09-14 6:34 GMT+02:00 Jorgen Simonsen <jorgen589.gmail.com>:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
==========================================
Lorenzo Gontrani
Research associate - EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email lorenzo DOT gontrani AT gmail DOT com
Webpage: http://webcaminiti/gontrani.html
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Received on Mon Sep 15 2014 - 01:00:02 PDT
