(unknown charset) [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff

From: (unknown charset) 辛志宏 <xzhfood.njau.edu.cn>
Date: Thu, 9 Jul 2020 12:11:32 +0800 (GMT+08:00)

The information is as follows when I run "loadoff MFA.lib", I also check the leap.log file, the information is the same.
> loadoff MFA.lib
Loading library: ./MFA.lib
Loading: UNK

I replaced MFA with UNK in the pdb file and inserted "TER" between ligand "UNK" and amino acid, new errors occured.


> mol = loadpdb DLP-499-cut-wat.pdb
Loading PDB file: ./DLP-499-cut-wat.pdb
-- residue 2048: duplicate [ H1] atoms (total 21)
-- residue 2048: duplicate [ H2] atoms (total 21)
-- residue 2048: duplicate [ O] atoms (total 21)
-- residue 2057: duplicate [ H1] atoms (total 2)
-- residue 2057: duplicate [ H2] atoms (total 2)
-- residue 2057: duplicate [ O] atoms (total 2)
-- residue 2064: duplicate [ H1] atoms (total 2)
-- residue 2064: duplicate [ H2] atoms (total 2)
-- residue 2064: duplicate [ O] atoms (total 2)
-- residue 2069: duplicate [ H1] atoms (total 5)
-- residue 2069: duplicate [ H2] atoms (total 5)
-- residue 2069: duplicate [ O] atoms (total 5)
-- residue 2071: duplicate [ H1] atoms (total 2)
-- residue 2071: duplicate [ H2] atoms (total 2)
-- residue 2071: duplicate [ O] atoms (total 2)
-- residue 2074: duplicate [ H1] atoms (total 3)
-- residue 2074: duplicate [ H2] atoms (total 3)
-- residue 2074: duplicate [ O] atoms (total 3)
-- residue 2078: duplicate [ H1] atoms (total 2)
-- residue 2078: duplicate [ H2] atoms (total 2)
-- residue 2078: duplicate [ O] atoms (total 2)
-- residue 2079: duplicate [ H1] atoms (total 17)
-- residue 2079: duplicate [ H2] atoms (total 17)
-- residue 2079: duplicate [ O] atoms (total 17)
-- residue 2104: duplicate [ H1] atoms (total 22)
-- residue 2104: duplicate [ H2] atoms (total 22)
-- residue 2104: duplicate [ O] atoms (total 22)
-- residue 2105: duplicate [ H1] atoms (total 243)
-- residue 2105: duplicate [ H2] atoms (total 243)
-- residue 2105: duplicate [ O] atoms (total 243)
-- residue 2038: duplicate [ H1] atoms (total 2)
-- residue 2038: duplicate [ H2] atoms (total 2)
-- residue 2038: duplicate [ O] atoms (total 2)
-- residue 2044: duplicate [ H1] atoms (total 2)
-- residue 2044: duplicate [ H2] atoms (total 2)
-- residue 2044: duplicate [ O] atoms (total 2)

Warning: Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)

Created a new atom named: OXT within residue: .R<VAL 339>

Warning: One sided connection. Residue (Cl-) missing connect0 atom.
  total atoms in file: 11460
  The file contained 1 atoms not in residue templates



I wond how to correct the errors, thank you in advance.

Zhihong Xin
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Received on Wed Jul 08 2020 - 21:30:03 PDT
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