From owner-chemistry "-at-" ccl.net Thu May 21 00:07:00 2015 From: "sulgi lim sulgi8941(_)gmail.com" To: CCL Subject: CCL: force field of amber14 Message-Id: <-51390-150520230157-12985-uF/iNo5GcWLCce+QB+dQNQ::server.ccl.net> X-Original-From: sulgi lim Content-Type: multipart/alternative; boundary=089e0158cba0e57e9c05168ec356 Date: Thu, 21 May 2015 12:01:51 +0900 MIME-Version: 1.0 Sent to CCL by: sulgi lim [sulgi8941.:.gmail.com] --089e0158cba0e57e9c05168ec356 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable To whom it may concern, This is Sulgi, a M.S. candidate and user of amber14. I=E2=80=99m writing to enquire about force field of amber14. When I tried to making new topology with my system, I read amber14 tutorials and did leap process using below command. Tleap =E2=80=93s =E2=80=93f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB Source leaprc.gaff Loadamberparams frcmod.ff99SB14 However, few days later, I found that force field reads parm10.dat. When I used amber11, parm99.dat was in log file formed by leap. Ph. D in my lab. let me know the right commands for ff99SB force field, but I am wondering if I can use my system based on parm10.dat. Is it a big difference or serious problem between parm10.dat and parm99.dat?? What is differences between the two? Could you please explain me? (If I send mail to wrong address, then please let me know.) Thank you for your consideration. Sincerely, Sulgi --089e0158cba0e57e9c05168ec356 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

= To whom it may concern,

=C2=A0

This is Sulgi, = a M.S. candidate and user of amber14.

=C2=A0

I=E2=80=99m writing to enquire about force field of amber1= 4.

When I tr= ied to making new topology with my system, I read amber14 tutorials and did= leap process using below command.

=C2=A0

Tleap =E2=80=93s =E2=80=93f $AMBERHOME/dat/leap/cmd/leaprc.ff= 14SB

Source le= aprc.gaff

Load= amberparams frcmod.ff99SB14

=C2=A0

However, few days later, I found that force field reads parm10.dat.<= /p>

When I used = amber11, parm99.dat was in log file formed by leap.

Ph. D in my lab. let me know the righ= t commands for ff99SB force field, but I am wondering if I can use my syste= m based on parm10.dat.

Is it a big difference or serious problem between parm10.dat and p= arm99.dat??

Wh= at is differences between the two?

Could you please explain me?

(If I send mail to wrong address, then = please let me know.)

=C2=A0

= Thank you for your consideration.

=C2=A0

Sincerely,

Sulgi

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