AMBER Archive (2009)

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

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Sep 04 2009 - 14:32:53 CDT

On Fri, Sep 04, 2009, Yikan Chen wrote:

> 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).

You would have to load gaff.dat and the TMS_model_mol2 file as well -- it's
not clear whether you did this or not.

> * 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 *

This is very strange: the mol2 file created by antechamber should have
atom types that use lower-case letters, but leap thinks that your atom types
are upper-case. Since you left out a lot of details of what you actually did,
it's hard to figure out what is going on. Be sure you have loaded the proper
files, and use the "desc" command in tleap to make sure that LEaP has residues
that are what you want.

...dac

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