Re: [AMBER] Joining two files

From: Lorenzo Gontrani <>
Date: Mon, 29 Oct 2012 15:32:47 +0100

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


2012/10/29 Jacopo Sgrignani <>:
>> 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

 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 Mon Oct 29 2012 - 08:00:03 PDT
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