Sorry.
The amoeba force-field simulation differ from the amber force-field
simulation. The .prmtop/.inpcrd for the latter could be directly from
tleap, but the .prmtop/.inpcrd for the former need to be converted using
tinker_to_amber.
Did I explain it clearly?
Elvis Martis <elvis.martis.bcp.edu.in> 于2018年12月11日周二 下午4:53写道：
> But what I did is the amoeba-parameter simulation as I mentioned above.
> The jac.prmtop/.inpcrd were not obtained directly from tleap, but converted
> from jac-amberFF.prmtop/inpcrd. So, how can I do it ?
>
> I don't quite understand what do you mean by converted "from
> jac-amberFF.prmtop/inpcrd"
>
>
> Best Regards
> Elvis A F Martis
> Molecular Simulations Group,
> Department of Pharmaceutical Chemistry,
> Bombay College of Pharmacy,
> Kalina, Santacruz [E],
> Mumbai 400098,
> INDIA.
> Institute Web-address: www.bcp.edu.in
> Research Group Web-address: www.profeccoutinho.net.in
> Personal Web-address: www.elvismartis.in
>
>
> ________________________________________
> From: 王茜茜 <wangqq430.gmail.com>
> Sent: 11 December 2018 12:23
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to get the jac.restrt？
>
> Dear Elvis A F Martis ,
> Thanks for your reply.
> But what I did is the amoeba-parameter simulation as I mentioned above.
> The jac.prmtop/.inpcrd were not obtained directly from tleap, but converted
> from jac-amberFF.prmtop/inpcrd. So, how can I do it ?
>
>
> qianqian
>
> Elvis Martis <elvis.martis.bcp.edu.in> 于2018年12月11日周二 下午12:48写道：
>
> > HI,
> > you get the restrt/inpcrd and prmtop from leap while you are preparing
> the
> > system.
> > The leap command is as follows
> > saveamberparm jac.prmtop jac.restrt
> > Hope this helps.
> >
> > Best Regards
> > Elvis A F Martis
> > Molecular Simulations Group,
> > Department of Pharmaceutical Chemistry,
> > Bombay College of Pharmacy,
> > Kalina, Santacruz [E],
> > Mumbai 400098,
> > INDIA.
> > Institute Web-address: www.bcp.edu.in
> > Research Group Web-address: www.profeccoutinho.net.in
> > Personal Web-address: www.elvismartis.in
> >
> >
> > ________________________________________
> > From: 王茜茜 <wangqq430.gmail.com>
> > Sent: 11 December 2018 09:07
> > To: amber.ambermd.org
> > Subject: [AMBER] How to get the jac.restrt？
> >
> > Dear developer,
> > Recently, I learned the pmemd.amoeba simulation using the JAC
> example
> > in /home/softwares/amber14/src/pmemd.amoeba/build_amoeba/examples/JAC. I
> > can successfully build the required files according to the tutorial.
> > BUT when submitting a task, in Run.amoeba_jac.pmemd (mpirun -np 8
> > /home/case/amber12/bin/pmemd.amoeba.MPI -O -i mdin -p jac.prmtop -c
> > jac.restrt -o jac_amoeba.pmemd.8.out), I can not obtain the restart file
> by
> > myself. Where does the jac.restrt come from or how to produce it using
> the
> > .prmtop and inpcrd?
> > Any suggestion will be grateful. Thanks!
> >
> >
> > Best regards!
> >
> > Qianqian
> > Macau university of science and technology
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Dec 11 2018 - 01:30:02 PST
