AMBER Archive (2009)

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

From: Yikan Chen (yc2r_at_virginia.edu)
Date: Fri Sep 04 2009 - 14:51:38 CDT

  Maybe you sent the wrong mail?...
  I will restate my problem:
  I have a big molecule that is composed with a short DNA duplex and two
short residues called TMS attaching on the both terminal of duplex. To make
this molecule recoginzed by Amber, I plan to convert a standard pdb file for
TMS to a mol2 file by antechamber, and load this mol2 file before I load the
pdb file of the big molecule. Will this method work? What kind of force
field should I choose? I am suggested to use GAFF for TMS and ff99SB for the
big molecule. I have no idea about how to do that.....
 Thanks for any help!

On Fri, Sep 4, 2009 at 2:33 PM, Rilei Yu <yulaomao1983_at_yahoo.com.cn> wrote:

> 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
>
> --- 0994գ, Yikan Chen <yc2r_at_virginia.edu> д
>
> : Yikan Chen <yc2r_at_virginia.edu>
> : [AMBER] Problem about adding a small residue to DNA
> ռ: "AMBER Mailing List" <amber_at_ambermd.org>
> : 200994,,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
>
> -----Ϊ-----
>
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