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
>>
>>
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>
>
>
> --
> ==========================================
> Lorenzo Gontrani
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> EDXD group of University of Rome "La Sapienza"
>
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Received on Wed Oct 31 2012 - 05:30:02 PDT
