Remove the CONECT records from your PDB. But probably better:
http://archive.ambermd.org/201405/#msg5
On Fri, 19 Feb 2016 19:12:20 +0900
홍종희 <croshong.nate.com> wrote:
>
> Dear AMBER users
>
> I'm now trying to generate parameters for FAD
>
> but it faills with following error sign
>
> [user1.hongserver FAD_temp]$ antechamber -i FAD_h.pdb -fi pdb -o
> FAD.mol2 -fo mol2 -c bcc -s 2
> Running: /usr/local/amber14/bin/bondtype -j
> full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f
> ac For atom[1]:P1, the best APS is not zero, bonds involved by this
> atom are frozen
> For atom[3]:P2, the best APS is not zero, bonds involved by this
> atom are frozen
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic double)Error: cannot run "/usr/local/amber14/bin/bondtype
> -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC
> -f ac" in judgebondtype() of antechamber.c properly, exit
>
> Is there anybody who knows what the above error means ?
>
> and Any kind of suggestion about how to solve this problem?
>
> Attached files are template PDB(FAD_h.pdb).
>
> Thanks
>
> [?usn=13646389&email=croshong.nate.com&key=b44dfca3102e28c191431c7d5dda702a$
> 2da3df6b.mail3.nate.com]
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Received on Fri Feb 19 2016 - 03:00:03 PST
