[AMBER] Missing Parameters

From: Melanie <journeywork.gmail.com>
Date: Tue, 15 Mar 2011 10:29:32 -0700

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Mar 15 2011 - 10:30:07 PDT
Custom Search