Re: [AMBER] MCPB settings file

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Tue, 22 Nov 2011 22:58:35 +0800

This is a multi-part message in MIME format.

--=====__1321973915.webmail__=====
MIME-Version: 1.0
Content-Type: text/plain; charset="UTF-8"


   Hi Ben,
             I have obtained manganese parameters that you can see in the
   attachment.I want to add manganese information in metalparm.xml and
   metals.xml.How could I write the value for PotenialWellDepth and
   hybridization in the metalParm.xml,about the value of
   bond12,bond13,bond14,bondAngle,bondLength,and bondTorsion I also want to
   know how to add these value.
              Best Regards
              JiYuan
   -------- åå§é®ä»¶ --------
   å件人: Ben Roberts <ben.roberts.geek.nz>
   åéæ¶é´: 2011-11-19 01:01
   æ¶ä»¶äºº: amber <amber.ambermd.org>
   ä¸»ãé¢: Re:Re: [AMBER] MCPB settings file
   Hi Ji-Yuan,
   On 18/11/2011, at 12:59 a.m., JiYuan Liu wrote:
> van der Waals parameters of the Manganese I have obtained by the website
   http://www.pharmacy.manchester.ac.uk/bryce/amber,I don't know how to put
   these MN2+ parameters into metalparm.xml and metals.xml,how should I solve
   this problem,and I will create manganese protein available by MCPB.
   Use the existing metal lines in metals.xml and metalParm.xml. Create copies
   of those lines, and change those parts of the copies that need to be changed
   (e.g., atom names and sigma and epsilon parameters). You should end up with
   a modified metals.xml and a modified metalParm.xml.
   Ben
   _______________________________________________
   AMBER mailing list
   AMBER.ambermd.org
   http://lists.ambermd.org/mailman/listinfo/amber

--=====__1321973915.webmail__=====
Content-Type: application/octet-stream;
        name="=?UTF-8?B?bW4uZnJjbW9k?="
Content-Transfer-Encoding: base64
Content-Disposition: attachment;
        filename="=?UTF-8?B?bW4uZnJjbW9k?="

Q2EyKyBhbmQgTW4yKyB2ZHcgcGFyYW1ldGVycyBmcm9tIENvbmNhbmF2YWxp
biBBIHN0dWR5Ck1BU1MKTU4gICAgIDU1LjAwICAgICAwLjAwICAgICAgICAK
Ck5PTkIKICBNTiAgICAgICAgMS42OTAwICAgICAwLjAxNDAKCg==

--=====__1321973915.webmail__=====
Content-Type: application/octet-stream;
        name="=?UTF-8?B?bW4ucHJlcA==?="
Content-Transfer-Encoding: base64
Content-Disposition: attachment;
        filename="=?UTF-8?B?bW4ucHJlcA==?="

ICAwICAwICAyCi0tLS0tLW1hbmdhbmVzZS0tLS0tLS0tLS0tLS0tCk1ORwpN
TkcgIElOVCAgMApDSEFOR0UgT01JVCBEVSAgQkVHCiAwLjAKICAgMSBEVU1N
ICBEVSAgTSAgMCAgLTEgIC0yICAwLjAwMCAgICAgMC4wMDAgICAgIDAuMDAw
ICAgIDAuMDAwCiAgIDIgRFVNTSAgRFUgIE0gIDEgICAwICAtMSAgMS4wMDAw
ICAgIDAuMDAwMCAgICAwLjAwMDAgICAwLjAwMAogICAzIERVTU0gIERVICBN
ICAyICAgMSAgIDAgIDEuMDAwMCAgIDkwLjAwMDAgICAgMC4wMDAwICAgMC4w
MDAKICAgNCBNTiAgICBNTiAgTSAgMjkuNjgzIDEyNy41NjEgLTE4LjQ1MCAg
Mi4wMAogCiAKRE9ORQpTVE9QCg==

--=====__1321973915.webmail__=====
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

--=====__1321973915.webmail__=====--
Received on Tue Nov 22 2011 - 07:00:03 PST
Custom Search