Hi
In the last steps if necessary see this
http://ambermd.org/tutorials/advanced/tutorial1_adv/
Best regards
Marcelo
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 9:18 GMT-03:00 Marcelo Andrade Chagas <andrade.mchagas.gmail.com>
:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Feb 26 2016 - 04:30:06 PST
