Hi David,
Many thanks for you help! It works.
Actually, I've tried amoeba with tinker and tinker_to_amber, although it is really slow. Anyway, it is another story.
Best,
Wei Ye, PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science,
Shanghai Jiaotong University,
800 Dongchuan RD, Shanghai, China.
Email: yw20055968.126.com
在2014年11月07 21时53分, "David A Case"<case.biomaps.rutgers.edu>写道:
On Fri, Nov 07, 2014, Wei Ye wrote:
> that under ff02pol.r1, I should
>
> > loadamberparams frcmod.pol3
> > set default IPOL 1
> > saveamberparm pdb test.top test.crd
You have to use "saveAmberParmPol" to create prmtop files for polarizable
force fields.
...hope this helps. It should be simpler, but Amber has *very* minimal
support for polarizable force fields, and ff02pol is more than a decade
old. There is some effort towards developmentof a new polarizable force
field, and its use will probably be simplified (and better documented)
once more users start trying to use it.
(Aside: Amber also supports Amoeba, but that it done by a very different
mechanism that does not involve LEaP.)
...dac
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Received on Fri Nov 07 2014 - 06:30:02 PST
