[AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped)

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Mon, 13 May 2019 16:56:06 +0100

I am trying to run protein ligand md using amber and I am following
following commands .I am receiving error messages as I am running commands
as follows:-

grep BG6 2bhl_clean.pdb > BG6.pdb
reduce BG6.pdb > BG6_h.pdb
antechamber -i BG6_h.pdb -fi pdb -o BG6_h.mol2 -fo mol2 -c bcc -s 2

Error message:
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.

antechamber -i BG6.pdb -o BG6.mol2 -fi pdb -fo mol2 -j 4 -at sybyl -dr no

Error message
udge bond type for Residue 2 with ID of 1508 and Name of BG6 ---
Warning: The assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    (be cautious, using a large value of PSCUTOFF (>100) will
    significantly increase the computation time).

 parmchk2 -i BG6_a.mol2 -f mol2 -o BG6_a.frcmod -s 2

Error message

Warning: Atom type (C.2) 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.2); set to 0.0.
         It is recommended to add the new atom type (C.2) to PARMCHK.DAT.
Warning: Atom type (O.2) 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.2); set to 0.0.
         It is recommended to add the new atom type (O.2) 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.
Warning: Atom type (C.1) 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.1); set to 0.0.
         It is recommended to add the new atom type (C.1) to PARMCHK.DAT.
Warning: Atom type (P.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 (P.3); set to 0.0.
         It is recommended to add the new atom type (P.3) to PARMCHK.DAT.
Warning: Atom type (O.co2) 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.co2); set to 0.0.
         It is recommended to add the new atom type (O.co2) to PARMCHK.DAT.
Segmentation fault (core dumped)

I am new to amber please anyone guide me.

Thank you
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Received on Mon May 13 2019 - 09:00:02 PDT
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