AMBER Archive (2009)

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

From: Yikan Chen (yc2r_at_virginia.edu)
Date: Sun Sep 06 2009 - 10:47:04 CDT

OK,I still do not know why I copy a wrong system message there.... When I
ran saveamberparm instruction, the message shown like this (other
instructions same as my former mail):

> test=loadpdb a.pdb
Loading PDB file: ./a.pdb
Illegal CONECT record in pdb file
  total atoms in file: 300
  Leap added 182 missing atoms according to residue templates:
       180 H / lone pairs
       2 unknown element
> saveamberparm test newff.prmtop newff.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -14.000000 is not zero.
 -- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: o - P
Could not find bond parameter for: o - P
Building angle parameters.
Could not find angle parameter: o - P - O2
Could not find angle parameter: o - P - O2
Could not find angle parameter: o - P - OS
Could not find angle parameter: c3 - o - P
Could not find angle parameter: o - P - O2
Could not find angle parameter: o - P - O2
Could not find angle parameter: o - P - OS
Could not find angle parameter: c3 - o - P
Building proper torsion parameters.
 ** No torsion terms for h1-c3-o-P
 ** No torsion terms for h1-c3-o-P
 ** No torsion terms for c3-o-P-O2
 ** No torsion terms for c3-o-P-O2
 ** No torsion terms for c3-o-P-OS
 ** No torsion terms for c3-c3-o-P
 ** No torsion terms for h1-c3-o-P
 ** No torsion terms for h1-c3-o-P
 ** No torsion terms for c3-o-P-O2
 ** No torsion terms for c3-o-P-O2
 ** No torsion terms for c3-o-P-OS
 ** No torsion terms for c3-c3-o-P
Building improper torsion parameters.
old PREP-specified impropers:
 <TMS 1>: C3 C2 C1 HE2
 <TMS 1>: C4 C1 C2 HE3
 <TMS 1>: C8 C7 C4 C2
 <TMS 1>: C4 C11 C7 HB6
 <TMS 1>: C14 C7 C11 O20
 <TMS 1>: C12 C11 C14 O21
 <TMS 1>: C14 C8 C12 O22
 <TMS 1>: C12 C4 C8 HB7
 <TMS 1>: C6 C5 C3 C1
 <TMS 1>: C3 C10 C6 HC5
 <TMS 1>: C6 C13 C10 HD9
 <TMS 1>: C3 C9 C5 HC4
 <TMS 1>: C5 C13 C9 HD8
 <TMS 1>: C15 C10 C13 C9
 <TMS 1>: C13 N1 C15 O1
 <TMS 1>: C16 C15 N1 H1
 <TMS 8>: C3 C2 C1 HE2
 <TMS 8>: C4 C1 C2 HE3
 <TMS 8>: C8 C7 C4 C2
 <TMS 8>: C4 C11 C7 HB6
 <TMS 8>: C14 C7 C11 O20
 <TMS 8>: C12 C11 C14 O21
 <TMS 8>: C14 C8 C12 O22
 <TMS 8>: C12 C4 C8 HB7
 <TMS 8>: C6 C5 C3 C1
 <TMS 8>: C3 C10 C6 HC5
 <TMS 8>: C6 C13 C10 HD9
 <TMS 8>: C3 C9 C5 HC4
 <TMS 8>: C5 C13 C9 HD8
 <TMS 8>: C15 C10 C13 C9
 <TMS 8>: C13 N1 C15 O1
 <TMS 8>: C16 C15 N1 H1
 total 102 improper torsions applied
 32 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

The problem is: I imported the residue prep file. However, how can I get the
bond parameters about bonds connecting the residue and DNA? like o-P bond in
the error message here? I will attach all the related files.
Thank you very much!

Best wishes!
Yikan

On Sun, Sep 6, 2009 at 8:30 PM, case <case_at_biomaps.rutgers.edu> wrote:

> On Sat, Sep 05, 2009, Yikan Chen wrote:
>
> > 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
> > be:
> > > mods=loadamberparams frcmod
>
> This is correct.
>
> > > 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)
>
> Looks like everything is working....dac
>
>
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  • chemical/x-pdb attachment: a.pdb


  • application/octet-stream attachment: TMS.prep

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