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)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> 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)
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Received on Mon Feb 29 2016 - 05:30:04 PST
