Here is the frcmod missing parameters
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
ca-cp-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
c3-o -c -o 1.1 180.0 2.0 General
improper torsional angle (1 general atom type)
ca-o -c -o 1.1 180.0 2.0 General
improper torsional angle (1 general atom type)
ca-ca-cp-cp 1.1 180.0 2.0 Using default
value
c -ca-ca-ca 1.1 180.0 2.0 Using default
value
ca-ca-ca-os 1.1 180.0 2.0 Using default
value
Should I load the frcmod and compound library file in the LEAP. Is the leap
program automatically resolve these missing parameters.
Kindly guide
On Thu, Sep 21, 2017 at 10:55 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> Dear Amber Users
>
> After extraction and reducing the bay compound, I prepared the mol2 file
> through Antechamber. But the problem is that when I check the sqm.pdb
> output file of antechamber it shows compound structure break and change
> while mol2 look good. Is this sqm.pdb affect the overall system, while I
> know we only use mol2 for further processing and production of frcmod,
> prmtop and incpred files.
>
> And when I reduced the compound i saw the warning like
>
> Building or keeping OH & SH Hydrogens.
> Rotating NH3 Hydrogens.
> Not processing Met methyls.
> WARNING: atom HAVA from 1DX will be treated as hydrogen
> WARNING: atom HAWA from 1DX will be treated as hydrogen
> SKIPPED H( 187 1DX H3 ): 187 1DX OAC bonds- 187 1DX CBG (short
> bond)
> SKIPPED H( 187 1DX H2 ): 187 1DX OAB bonds- 187 1DX CBH (short
> bond)
>
>
> Are these warning skipped H affect the system? or I can ignore these kind
> of warning.
>
> Kind Regards
>
>
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Received on Thu Sep 21 2017 - 11:30:03 PDT
