if you look below I think Dan Roe already answered this question. Also if
you want more help than he gave you, then you'd need to give the info he
asked about.
On Mon, Feb 29, 2016 at 8:13 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
wrote:
> Dear all,
> I have prepared the DNA via Amber as a PDB file, then I am going to
> convert it to Mol2, but it is beyond the max atom and I encountered errors.
> What should I do, to solve this problem? :(
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Friday, February 26, 2016 4:47 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Pdb file to Mol2
>
> Hi,
>
> I don't know offhand what a TIW simulation is. Can you be more
> specific about your system (name, PDB ID, etc), and what the goal of
> your study is?
>
> -Dan
>
> On Fri, Feb 26, 2016 at 8:30 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > 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)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 29 2016 - 06:00:04 PST
