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.virginia.edu> 写道：
发件人: Yikan Chen <yc2r.virginia.edu>
主题: [AMBER] Problem about adding a small residue to DNA
收件人: "AMBER Mailing List" <amber.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
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Received on Mon Sep 14 2009 - 11:47:26 PDT
