AMBER Archive (2009)

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

From: Yikan Chen (
Date: Thu Sep 03 2009 - 23:33:52 CDT

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
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?
  1X6W.pdb: the molecule I am working on


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