Hello,
I have been generating .prmtop and .inpcrd files using the PDB:3AYD. It has
a modified glycan molecule as there is a bond between A2G and NPO. I did
antechamber for the whole ligand molecule. But, I faced the following error.
Welcome to antechamber 19.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: This molecule has no hydrogens nor halogens.
It is quite possible that there are unfilled valences.
-- Check Geometry --
for those bonded
for those not bonded
Warning: Close ( 1.44) nonbonded atoms (ID: 2, Name: C1) and (ID: 32, Name:
OH).
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
/home/lucy/software/amber18/amber18/bin/to_be_dispatched/antechamber: Fatal
Error!
This molecule may have more than one unit.
antechamber can only handle one unit. If the input is a single unit
then the connectivity is wrong and the geometry may be bad.
Please convert your molecule to a mol2 file via:
antechamber -j 5 -at sybyl -dr no
And then check your molecule with a visualization program;
manually add missing bonds or delete unwanted bonds as appropriate.
I used the above command to produce the mol2 file and then manually added a
bond between NPO and A2G using pymol. But, there was a lot of warning while
generating the .frcmod file.
Warning: Atom type (C.3) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
Warning: No mass information for atom type (C.3); set to 0.0.
It is recommended to add the new atom type (C.3) to PARMCHK.DAT.
Warning: Atom type (N.3) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
Warning: No mass information for atom type (N.3); set to 0.0.
It is recommended to add the new atom type (N.3) to PARMCHK.DAT.
Warning: Atom type (O.3) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
Warning: No mass information for atom type (O.3); set to 0.0.
It is recommended to add the new atom type (O.3) to PARMCHK.DAT.
It generated the .frcmod file but could not generate the .prmtop file
through tleap.
Please help me with this.
Thank you!
--
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Received on Sun Mar 17 2024 - 04:00:02 PDT
