(Note that the obsolete prepin IMPROPER section is just quoted for help in
deriving improper params in the newer form. In this case one would just
load the residue in question, perhaps with immediate neighbors if a chain
residue.)
Bill
Rejwan <rejwan_88.yahoo.com> wrote:
> 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
>
> ======
> REJWAN ALI
> MOUNT SINAI, NEW YORK, NY
> Email
>
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Received on Wed Jun 19 2013 - 14:00:03 PDT
