Dear Marco, I guess that the molecule you want to use is not an
"ordinary" organic molecule, so that gaff atom-type cannot be
assigned. It should not be a format problem.
You can try playing with antechamber options (-j 0 or - j 5), or
possibly passing through mol2 files.
You can also modify the definition file
$AMBERHOME/dat/antechamber/ATOMTYPE_GFF.DEF, and create your own atom
types.
if you want, you can send me the file, I will see if I can help you somehow.
All the best
Lorenzo
2012/10/31 Marco Malvaldi <marcoampelio.hotmail.com>:
> Thanks Lorenzo, prep format is more friendly... Now I'm facing a digferent problem with hydrogens. When processing My pdb for an organic molecole with antechamber, all hydrogens are replaced by X and set in a nonsense geometry. The same happens with sdf and mol format... Ant. Suggestion?
>
> Grazie
> Marco
>
>
> Inviato da iPhone
>
> Il giorno 29/ott/2012, alle ore 15:33, "Lorenzo Gontrani" <l.gontrani.caspur.it> ha scritto:
>
>> Dear Marco, probably you will find the PREP format more user-fiendly
>> than LIB (a.k.a. OFF) format.
>> You can easily convert a PDB file into PREP format with antechamber.
>>
>> I found it important to load PREP files as the first thing; than the
>> potential (i. e. GAFF) and then the modified FRCMOD, to let tleap
>> memorize the latest changes.
>> Then you can also define a new unit, and eventually load a PDB/MOL2
>> file with the structure, paying attention that atom names are exactly
>> the same of PREP file.
>> Let me know if it works or if you need.
>>
>> All the best, and ciao
>>
>> Lorenzo
>>
>> 2012/10/29 Jacopo Sgrignani <sgrigna.sissa.it>:
>>>> Dear Marco
>>> when you created the prmtop file for graphene and for ligand did you upload a lib files?
>>> Why don't you upload the two lib files also when you combine them to form the complex?
>>> In my experience the one-to-one correspondence is encoded in the lib files.
>>>
>>> Moreover you use gaff and then maybe you have to upload also gaff before to form the complex.
>>> source leaprc.ff99SB
>>> source leaprc.gaff
>>>
>>>
>>> Ciao
>>>
>>> Jacopo
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> ==========================================
>> Lorenzo Gontrani
>> Research associate of CNR-ISM (Rome Tor Vergata)
>> EDXD group of University of Rome "La Sapienza"
>>
>> GSM +39 338 7615798
>> Email l DOT gontrani AT caspur DOT it
>> Webpage: http://webcaminiti/gontrani.html
>> =========================================
>>
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>
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--
==========================================
Lorenzo Gontrani
Research associate of CNR-ISM (Rome Tor Vergata)
EDXD group of University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
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Received on Wed Oct 31 2012 - 06:00:04 PDT
