Dear Ravi,
> Can you please suggest me which files i have to modify in antechamber.
> It will be a great help.
Personally, I proceed as it follows:
-1 run R.E.D. to generate a FF library (mol2 file format) and/or a
molecule/molecular fragment
-2 add the FF atom types I want in the mol2 file; display the
structure in LEaP/VMD to check charge equivalencing, the molecular
topology, the atom names etc...
-3 manually create a frcmod file (if needed) in agreement with the FF
atome types and FF I selected
-4 load all in LEaP
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
regards, Francois
> On Wed, Nov 28, 2012 at 11:35 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Ravi,
>>
>> You need to create a new FF atom type and a new frcmod file manually.
>>
>> regards, Francois
>>
>>
>> > I have a molecule which is having a oxygen connected with three atoms.
>> > Since there is no bond type defined for such a system in antechamber,
>> > running antechamber giving following error.-
>> >
>> > For atom[1]:O1, the best APS is not zero, exit
>> >
>> > Error: cannot run "/usr/local/amber9/exe/bondtype -i
>> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
>> > judgebondtype() of antechamber.c properly, exit
>> >
>> > Can anybody help me in this regards, like how to modify the antechamber
>> > files or anything else.
>> > Any help will be highly appreciated.
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Received on Wed Nov 28 2012 - 01:30:02 PST
