[AMBER] Fatal error atom type work around

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Mon, 31 Aug 2020 19:32:19 +0800

Dear all,
I would like to share my experience on the above error. I had this error
even when I followed the correct list of commands. My work around was like
 1.Separate protein ligand complex using Discovery Studio (very convenient)
or grep command as is useful
 2. send ligand with hydrogens added to RESP server for charge calculation
3. convert ligand file to mol2 file using DS or pymol or chimera
4. parse ligand.mol2 file to antechamber using to get the gaff atom type.
Previously I could use the RED server mol2 file with antechamber. However,
now I could not as it kept giving me the "unfulfilled valance" error. So
the work around was very helpful.
4. Use the RESP charges to replace any charges that may be generated by the
antechamber program in the ligand.mol2 file and use this final prepared
file to generate the lig.lib, ligand.prmtop and ligand.rst7 files. the
frcmod.known generated by RED server can be used for the parameters. Need
to convert all atom types in the file to gaff
5. For complex preparation I used the following commands.
    pdb4amber -i complex.pdb -o complex_prep.pdb --reduce
   tleap -f leaprc.protein.ff14SB
    source leaprc.gaff
    set default PBRadii mbondi3
    loadmol2 ligand.mol2
    loadamberparams frcmod.lig
    loadoff lig.lib
    complex = loadpdb complex_pre.pdb
    source leaprc.water.tip3p
    loadamberparams frcmod.ionsjc_tip3p

I did not get any error until the end after this. The ligand loaded

Not sure if this is can work for anyone but it it did work for me. The only
hassle now is the conversion of mol2 file generated by the RED server into
mol2 file with gaff atom types.
I hope the developers could look into it.

Thank you everyone especially Dr. Case who responded promptly to several
Ayesha Fatima
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Received on Mon Aug 31 2020 - 05:00:02 PDT
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