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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Received on Tue Mar 15 2011 - 11:30:05 PDT
