Re: [AMBER] Missing Parameters

From: Melanie <journeywork.gmail.com>
Date: Thu, 17 Mar 2011 12:27:35 -0700

Hi Ilyas,
This should be a regular system. I am using a structure from the PDB; I have
attached it. As a background, I edited 3NJW_old to 3NJW by changing the CYS
to CYX, since the structure contains a cysteine disulfide bond. This edit
fixed some of the original errors I had regarding that particular bond.
If I were to treat this as a regular system, how would I change the
structure? And if I have to define my own residue library, would I be using
the addPdbResMap function or something else?

Thanks very much,
Melanie

On Tue, Mar 15, 2011 at 11:18 AM, Ilyas Yildirim <
i-yildirim.northwestern.edu> wrote:

> Melanie - It seems that you have a system where you have a bond (in the
> atom type notation) N3-C. I checked out parm99.dat and there is not any
> such bond defined. As a result, you need to defined those missing
> parameters. Is this a regular system or do you have your own residue
> library defined, which you want to use in this particular system?
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
>
> On Tue, 15 Mar 2011, Melanie wrote:
>
> > Hi all,
> > I've been trying to figure out what is wrong with my molecule. This set
> of
> > missing parameters appears to be stemming from one particular bond or
> area.
> > When leap would not save my parameter files because of these errors, I
> tried
> > to figure out which parameters I was missing by using parmchk and
> > antechamber; unfortunately, both of these also ended with an error
> message.
> > I also tried addIons, to no avail. Can someone please tell me how to fix
> > this, and also *how to detect certain basic errors that may cause a
> > parameter file to not be saved*, etc.
> > I have pasted the missing parameters error and antechamber errors below,
> as
> > well as attached the leap.log file.
> >
> > *> saveamberparm njw njw.prmtop njw.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.*
> > *Could not find bond parameter for: N3 - C*
> > *Building angle parameters.*
> > *Could not find angle parameter: CT - N3 - C*
> > *Could not find angle parameter: H - N3 - C*
> > *Could not find angle parameter: H - N3 - C*
> > *Could not find angle parameter: H - N3 - C*
> > *Could not find angle parameter: N3 - C - CT*
> > *Could not find angle parameter: N3 - C - O2*
> > *Could not find angle parameter: N3 - C - O2*
> > *Building proper torsion parameters.*
> > * ** No torsion terms for CT-N3-C-CT*
> > * ** No torsion terms for CT-N3-C-O2*
> > * ** No torsion terms for CT-N3-C-O2*
> > * ** No torsion terms for H-N3-C-CT*
> > * ** No torsion terms for H-N3-C-O2*
> > * ** No torsion terms for H-N3-C-O2*
> > * ** No torsion terms for H-N3-C-CT*
> > * ** No torsion terms for H-N3-C-O2*
> > * ** No torsion terms for H-N3-C-O2*
> > * ** No torsion terms for H-N3-C-CT*
> > * ** No torsion terms for H-N3-C-O2*
> > * ** No torsion terms for H-N3-C-O2*
> > *Building improper torsion parameters.*
> > * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
> > * atoms are: CG CE2 CD2 CE3*
> > * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
> > * atoms are: NE1 CZ2 CE2 CD2*
> > * ** Warning: No sp2 improper torsion term for CT-O2-C-N3*
> > * atoms are: CB OD1 CG N*
> > * ** Warning: No sp2 improper torsion term for CT-O2-C-N3*
> > * atoms are: CB OD2 CG N*
> > * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
> > * atoms are: CG CE2 CD2 CE3*
> > * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
> > * atoms are: NE1 CZ2 CE2 CD2*
> > * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
> > * atoms are: CG CE2 CD2 CE3*
> > * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
> > * atoms are: NE1 CZ2 CE2 CD2*
> > * total 62 improper torsions applied*
> > *Building H-Bond parameters.*
> > *Parameter file was not saved.*
> >
> > --------------------------
> >
> > *[.login2 ~]$ $AMBERHOME/exe/antechamber -i
> /u/home/campus/template/3NJW.pdb
> > -fi pdb -o njw.prepin -fo prepi -c bcc -s 2*
> > *Running: /u/home2/ppk/amber10/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac*
> > *sh: /u/home2/ppk/amber10/bin/bondtype: Permission denied*
> > *Error: cannot run "/u/home2/ppk/amber10/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit*
> >
> >
> >
> > Thank you,
> > Melanie
> >
>
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>



-- 
********
Minnie
********




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Received on Thu Mar 17 2011 - 12:30:02 PDT
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