Hi
I know use antechamber and bcc formalism wheel MOPAC the program (make a
small optimization to generate loads). This
is the number of atoms of limitation.
I've read that you can modify it.
But first I suggest the following:
use antechamber without putting the command line -c bcc
MHA:amber14 mha$ $AMBERHOME/bin/antechamber -i Part.pdb -fi pdb -o
Part.mol2 -fo mol2 -s 2
this when I generate a .mol2 file without charges
then u can use R.E.D to calculate RESP loads required in Amber force fields
After that use parmchk and manages the file .frcmod your system
load them in xleap
follow the sequence to edit your file suggest see the following tutorial (
http://ambermd.org/tutorials/basic/tutorial4b/)
add the RESP charges in xleap
then you can save the file as you want
savepdb AAA AAA.pdb
savemol2 AAA AAA.mol2
saveoff AAA AAA.lib
for example
Best regards
Marcelo
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Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-02-26 9:03 GMT-03:00 Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>:
> Hi,
> I use the following command for converting Part.pdb file to Part.Mol2,
>
> MHA:amber14 mha$ $AMBERHOME/bin/antechamber -i Part.pdb -fi pdb -o
> Part.mol2 -fo mol2 -c bcc -s 2
>
>
> But, I received the following warnings and errors :(
>
>
> 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.
>
> Continuing, but problems may be encountered.
>
>
> The atom number exceeds the MAXATOM, reallocate memoryWarning: detected
> more than 10 Residue sequence numbers;
>
> this may be a large multiple residue PDB file;
>
> large multiple residue PDB files are not supported.
>
> Continuing, but problems may be encountered.
>
>
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> Running: /Users/amber14/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0
> -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
>
> ^CError: cannot run "/Users/amber14/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
>
>
>
> would you please give me some suggestions to resolve it, or alternatives
> to convert pdb file to Mol2?
>
> Bests
>
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Received on Fri Feb 26 2016 - 04:30:05 PST
