Hi,
My pdb file has a protein and a ligand (no
bond between these).
I made a prepi file for the ligand using antechamber.
When I try to save the .top and .crd file in Leap
( I am using parm99.dat)
using saveAmberParm I am getting the following warnings.
--------------------------------------------------------
** Warning: No sp2 improper torsion term for H-H-N3-CT
atoms are: H2 H3 N CD
** Warning: No sp2 improper torsion term for H-H-N3-CT
atoms are: H2 H3 N CA
** Warning: No sp2 improper torsion term for H-CT-N3-CT
atoms are: H2 CD N CA
** Warning: No sp2 improper torsion term for H-CT-N3-CT
atoms are: H3 CD N CA
** 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-H-N3-H
atoms are: CE HZ1 NZ HZ2
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ1 NZ HZ3
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ2 NZ HZ3
** Warning: No sp2 improper torsion term for H-H-N3-H
atoms are: HZ1 HZ2 NZ HZ3
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ1 NZ HZ2
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ1 NZ HZ3
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ2 NZ HZ3
** Warning: No sp2 improper torsion term for H-H-N3-H
atoms are: HZ1 HZ2 NZ HZ3
** 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-H-N3-H
atoms are: CE HZ1 NZ HZ2
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ1 NZ HZ3
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ2 NZ HZ3
** Warning: No sp2 improper torsion term for H-H-N3-H
and Finally it says
old PREP-specified impropers:
<199>: C6 C1 C7 C8
<199>: C3 C7 C1 O2
<199>: C4 C1 C3 H80
<199>: C3 C5 C4 H81
<199>: C4 C6 C5 H82
<199>: C9 C5 C6 C7
<199>: C6 N11 C9 O10
<199>: C15 C19 C14 C13
<199>: C14 C16 C15 H89
<199>: C15 C17 C16 H90
<199>: C16 C18 C17 H91
<199>: C17 C19 C18 H92
<199>: C14 C18 C19 H93
<199>: C20 N24 C22 O23
<199>: C30 N33 C31 O32
<199>: C36 C40 C35 C34
<199>: C35 C37 C36 C41
<199>: C36 C38 C37 H107
<199>: C37 C39 C38 H108
<199>: C38 C40 C39 H109
<199>: C35 C39 C40 H110
total 575 improper torsions applied
21 improper torsions in old prep form
------------------------------------------------
It does save the .top and .crd files.
What are those warnings? Is anything wrong?
no SP2 improper for H-H-N3-CT is not clear to me since
both N3 and CT are SP3.
Pradipta
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Received on Thu Apr 08 2004 - 13:53:00 PDT
