AMBER Archive (2009)

Subject: 回复： [AMBER] Problem about adding a small residue to DNA

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Fri Sep 04 2009 - 01:33:50 CDT

Dear Prof. David,

This afternoon, I talked too much to you. I know you are really very busy, next time I will discuss my problem in a more appropriated way. For example in the meeting and our discussion time. I think that will be enough. Thanks for your recommendation to the lecturer this afternoon.

PhD road is not so smooth, I know, there are also far way for me to go.  So every hour I have to prepare to face the challenge in my experiment.

Thanks for your help!

Having a good weekend.

Rilei Yu

--- 09年9月4日，周五, Yikan Chen <yc2r_at_virginia.edu> 写道：

发件人: Yikan Chen <yc2r_at_virginia.edu>
主题: [AMBER] Problem about adding a small residue to DNA
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年9月4日,周五,下午12:33

Hi Amber users,
  The substance I am working on is a small residue called TMS combing with
an DNA duplex. In order to make the TMS part recognized by Amber, I also
download a pdb file for TMS, and do the following things:
antechamber -i TMS_model.pdb -fi pdb -o TMS_model.mol2 -fo mol2 -c bcc -nc
-1
parmchk -i TMS_model.mol2 -f mol2 -o frmod
  Everything is fine for these instructions.
  However, it does not work quite well for loadpdb instruction(in ff99SB).
There will be error message:
*  test=loadpdb 1X6W-H-ok-con.pdb *
*  Loading PDB file: ./1X6W-H-ok-con.pdb *
*  One sided connection. Residue: missing connect1 atom. *
*  One sided connection. Residue: missing connect1 atom. *
*  total atoms in file: 300 Leap added 182 missing atoms according to
residue templates: 182 H / lone pairs*
  And cannot saveamberparm:
 * WARNING: The unperturbed charge of the unit: -14.000000 is not zero. *
*  -- ignoring the warning. Building topology. Building atom parameters. *
*  For atom: .R<TMS 1>.A<C1 1> Could not find type: CE *
*  For atom: .R<TMS 1>.A<C20 3> Could not find type: C3 *
*  For atom: .R<TMS 1>.A<C21 5> *
  ...
  What is the meaning of these?
  Also what is more important is I am puzzled about how to choose force
field. It is said I should use gaff for TMS residue and ff99SB for this
molecule. How can I do that? Does antechamber work for this situation?
  Attachment:
  1X6W.pdb: the molecule I am working on

  Thanks!
  Best,
  Yikan

-----下面为附件内容-----

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

      ___________________________________________________________
  好玩贺卡等你发，邮箱贺卡全新上线！
http://card.mail.cn.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber