From owner-chemistry: at :ccl.net Sat Dec 1 13:42:00 2018 From: "Kshatresh Dutta Dubey kshatresh##gmail.com" To: CCL Subject: CCL: MD simulation program for saturated enzyme reaction Message-Id: <-53566-181201134118-26708-uP6aqdJraeWRpjFrLF0hqg/./server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary="000000000000969a23057bfa4213" Date: Sat, 1 Dec 2018 19:41:00 +0100 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh#gmail.com] --000000000000969a23057bfa4213 Content-Type: text/plain; charset="UTF-8" Hi kjh950429, The quality of MD simulation doesn't depend upon the MD engines such as NAMD, Amber, Gromacs etc but it depends upon the force field used. Note that NAMD, AMBER, Hyperchem as you mentioned, are MD engines. You can use any of the above programs depending upon its availability for you. In my personal opinion (for enzymes), I suggest Amber and Charmm forcefields. NAMD is free and it supports both forcefields. Amber MD program (sander) is free but as AmberTools. If you want more speedy calculations with amber, i.e. pmemd, you have to buy Amber. Hope it helps. Kshatresh On Sat, Dec 1, 2018 at 7:39 PM Kshatresh Dutta Dubey wrote: > Hi kjh950429, > > The MD simulation doesn't depend upon the MD engines such as NAMD, Amber, > Gromacs etc but it depends upon the force field used. Note that NAMD, > AMBER, Hyperchem as you mentioned, are MD engines. You can use any of the > above programs depending upon its availability for you. In my personal > opinion (for enzymes), I suggest Amber and Charmm forcefields. NAMD is free > and it supports both forcefields. Amber MD program (sander) is free but as > AmberTools. If you want more speedy calculations with amber, i.e. pmemd, > you have to buy Amber. > > Hope it helps. > Kshatresh > > On Sat, Dec 1, 2018 at 7:28 PM kjh950429^_^gmail.com < > owner-chemistry---ccl.net> wrote: > >> >> Sent to CCL by: " " [kjh950429:_:gmail.com] >> Hi everyone. >> I am currently planning on running a MD simulation for completely >> saturated enzymes >> (to be more specific, enzymes comprised of about 2,000 or so atoms such >> as bovine >> liver rhodanese.) I was wondering which program would be best suited to >> run the >> job: NAMD, AMBER, Hyperchem etc.>> >> >> > > -- > With best regards > > ************************************************************************************************ > Dr. Kshatresh Dutta Dubey > Researcher, > Institute of Cell and Molecular Biology > Uppsala University > Uppsala, Sweden > > > -- With best regards ************************************************************************************************ Dr. Kshatresh Dutta Dubey Researcher, Institute of Cell and Molecular Biology Uppsala University Uppsala, Sweden --000000000000969a23057bfa4213 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi=C2=A0 kjh950429,

The quality of MD s= imulation doesn't depend upon the MD engines such as NAMD, Amber, Groma= cs etc but it depends upon the force field used. Note that=C2=A0 NAMD, AMBE= R, Hyperchem as you mentioned, are MD engines. You can use any of the above= programs depending upon its availability for you. In my personal opinion (= for enzymes), I suggest Amber and Charmm forcefields. NAMD is free and it s= upports both forcefields. Amber MD program (sander) is free but as AmberToo= ls. If you want more speedy calculations with amber, i.e. pmemd, you have t= o buy Amber.

Hope it helps.
Kshatresh

On Sat, Dec 1, 201= 8 at 7:39 PM Kshatresh Dutta Dubey <kshatresh---gmail.com> wrote:
Hi=C2=A0 kjh950429,

The MD simulatio= n doesn't depend upon the MD engines such as NAMD, Amber, Gromacs etc b= ut it depends upon the force field used. Note that=C2=A0 NAMD, AMBER, Hyper= chem as you mentioned, are MD engines. You can use any of the above program= s depending upon its availability for you. In my personal opinion (for enzy= mes), I suggest Amber and Charmm forcefields. NAMD is free and it supports = both forcefields. Amber MD program (sander) is free but as AmberTools. If y= ou want more speedy calculations with amber, i.e. pmemd, you have to buy Am= ber.

Hope it helps.
Kshatresh

On Sat, Dec 1, 2018 at 7:2= 8 PM kjh950429^_^gmail.com <owner-c= hemistry---ccl.net> wrote:
Sent to CCL by: "=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0" [kjh9= 50429:_:g= mail.com]
Hi everyone.
I am currently planning on running a MD simulation for completely saturated= enzymes
(to be more specific, enzymes comprised of about 2,000 or so atoms such as = bovine
liver rhodanese.) I was wondering which program would be best suited to run= the
job: NAMD, AMBER, Hyperchem etc.



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--
=
With best regards
*************************= ***********************************************************************
= Dr. Ksh= atresh Dutta Dubey
Researcher,
Institute of Cell = and Molecular Biology
Uppsala University
Uppsala, S= weden




--
= With best regards
***********************************************= *************************************************
Dr. Kshatresh Dutta Dubey
Researcher,
Institute of Cell and Molecular Biology
Uppsala University
Uppsala, Sweden
=

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