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: $B2&0+0+(B <wangqq430.gmail.com>
Sent: 11 December 2018 12:23
To: amber.ambermd.org
Subject: Re: [AMBER] How to get the jac.restrt$B!)(B
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> $BP2(B2018$BG/(B12$B7n(B11$BF|<~Fs(B $B2<8a(B12:48$B<LF;!'(B
> 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: $B2&0+0+(B <wangqq430.gmail.com>
> Sent: 11 December 2018 09:07
> To: amber.ambermd.org
> Subject: [AMBER] How to get the jac.restrt$B!)(B
>
> 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
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Received on Tue Dec 11 2018 - 01:00:03 PST
