I'm trying to make the topology file of a ligand-protein system.
In tLeap suit of Amber I fed both .prepin and .frcmod of the ligand, I used RESP charge obtained via Gaussian 09 Geometry Optimization for PREPIN file. The .frcmod file was created by parmchk routine.
The tLeap error showed only 2 out of 10 torsion terms could be implemented. Could you please help how can I extract the missing Angle and Torsion terms ? Also where should I plug the terms (Is it in the .frmod file ?) to rerun Leap ? I'm copying the error screen.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: o - c2 - n
Could not find angle parameter: n - c2 - o
Could not find angle parameter: c1 - c2 - n
Could not find angle parameter: os - c2 - o
Could not find angle parameter: c1 - os - c2
Could not find angle parameter: c2 - c1 - os
Building proper torsion parameters.
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 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
** 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 c1-c3-c2-c1
atoms are: C16 C7 C10 C17
** Warning: No sp2 improper torsion term for c2-c1-c2-c1
atoms are: C3 C15 C9 C14
** Warning: No sp2 improper torsion term for n-c2-c2-c2
atoms are: N6 C9 C3 C1
** Warning: No sp2 improper torsion term for n-o-c2-n
atoms are: N5 O12 C4 N6
** Warning: No sp2 improper torsion term for c2-c1-c2-n
atoms are: C1 C22 C2 N5
** Warning: No sp2 improper torsion term for c2-c2-c2-c2
atoms are: C8 C2 C1 C3
** Warning: No sp2 improper torsion term for os-o-c2-c2
atoms are: O11 O13 C8 C1
** Warning: No sp2 improper torsion term for c1-c1-c2-c1
atoms are: C24 C21 C23 C25
old PREP-specified impropers:
: C25 C24 C23 C21
: C1 O13 C8 O11
: C8 C2 C1 C3
: C22 C1 C2 N5
: C2 C4 N5 H30
: N5 N6 C4 O12
: C4 C3 N6 H31
: C1 C9 C3 N6
: C15 C14 C9 C3
: C17 C16 C10 C7
total 1330 improper torsions applied
10 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
Thank you.
Rejwan
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REJWAN ALI
MOUNT SINAI, NEW YORK, NY
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Received on Tue Jun 18 2013 - 13:30:04 PDT
