AMBER Archive (2009)

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

From: Yikan Chen (
Date: Fri Sep 04 2009 - 16:38:27 CDT

Sorry.... Here is how it is going:
  I have got the TMS.mol2 and frcmod files without problems(with antechamber
and parmchk).
  then: enter tleap with ff99SB

> source leaprc.gaff
----- Source: /itc/apps/amber/10/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /itc/apps/amber/10/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /itc/apps/amber/10/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,

> TMS=loadmol2 TMS.mol2
Loading Mol2 file: ./TMS.mol2
Reading MOLECULE named TMS

> 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
then I will saveamberparm test newff.prmtop newff.inpcrd. There will be the
error message I said.
Actually I do not know how to use frcmod file(I do not quite understand the
meaning of P70-71 of Ambertools manual), if I do what they said, there will
> mods=loadamberparams frcmod
Loading parameters: ./frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveamberparm TMS prmtop inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
 -- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 16 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:
        res total affected
        TMS 1
 (no restraints)

  Thank you for your furthur help:)

On Sat, Sep 5, 2009 at 4:37 AM, case <> wrote:

> On Sat, Sep 05, 2009, Yikan Chen wrote:
> > Could not find angle parameter: c3 - c3 - o
> ..etc. Did you load the gaff.dat and frcmod files created by antechamber
> and
> parmchk? As before, when you only post a little bit of what you actually
> did,
> it is very hard to trouble-shoot problems.
> ....dac
> _______________________________________________
> AMBER mailing list

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