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 - 11:00:03 PDT
