I have taken a protein and because of its larger size I have taken the residues around the active center. Because of this, there are missing residues and the residues are not in chain. I want to run MD simulation for this modelled protein but in the first step of generating mol2 files using antechamber, I am getting a fatal error as follows:
Welcome to antechamber 21.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb File --
Status: pass
Warning: Detected more than 10 Residue sequence numbers;
this may be a large multiple residue PDB file;
large multiple residue PDB files are not supported.
This warning usually indicates a conceptual misunderstanding.
We recommend reviewing the Information flow in Amber documentation
and the antechamber tutorials.
Continuing, but problems may be encountered.
Info: The number of atoms (2560) exceeded MAXATOM.
Warning: Detected more than 10 Residue sequence numbers;
this may be a large multiple residue PDB file;
large multiple residue PDB files are not supported.
This warning usually indicates a conceptual misunderstanding.
We recommend reviewing the Information flow in Amber documentation
and the antechamber tutorials.
Continuing, but problems may be encountered.
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
/opt/amber20-mpi/amber20/bin/antechamber: line 9: 14993 Segmentation fault (core dumped) $AMBERHOME/bin/wrapped_progs/antechamber "$@"
I am doing this from antechamber tutorial: http://ambermd.org/tutorials/basic/tutorial4b/
How can I do antechamber with my protein?
Thanks in advance
Regards
Purva
To simulate a region of interest rather than the whole protein, do not modify the protein but use nonperiodic boundary conditions (sphere); everything outside the sphere should be restrained and not included in nonbonded interactions with the simulated system.
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