Hi, I am going to use it for TIW simulation. Is it eligible to use cpptraj command?
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Friday, February 26, 2016 4:20 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Pdb file to Mol2
Hi,
On Fri, Feb 26, 2016 at 5:03 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk> wrote:
> 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
What is your ultimate goal here? If the goal is just to convert from
PDB to Mol2 format you can just use cpptraj:
cpptraj -p Part.pdb -y Part.pdb -x Part.mol2
However, if you are trying to generate parameters for a molecule it
seems like Part.pdb is far too big and will need to be split into
subunits somehow. If you give some more details about what your
ultimate goal is we may be able to help further.
-Dan
>
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Feb 26 2016 - 08:00:04 PST
