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
