Dear all,
is the SCEE for electrostatics and SCNB for VDW 1-4 interactions written in the prmtop file ... for GAFF
also in the amb2grmx.pl these VALUES are defaulted to the one used for GAFF ....0.5 VDW, 0.83 EEL
This script converts Amber topology file to gromacs ..is this possible !
MANY THANKS
Fati
________________________________
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Wed 21/07/2010 14:09
To: AMBER Mailing List
Subject: Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
On Wed, Jul 21, 2010, kamlesh sahu wrote:
>
> I am using amber 10 to simulate small molecules (modified a little as
> compared to original pdb structure). First I used antechamber to fit ligand
> parameters and then I used tleap to generate library in this way -
> ~/src/Xtruct/trunk/amber_10_install/bin/antechamber -i DXQ-11_h.pdb -fi pdb
> -o DXQ-11.mol2 -fo mol2 -c bcc -s 2 -j 5 -nc +2
>
>
> It gives error messages -
>
> FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
This generally means that atom or residue names in the pdb file don't match
those in the DXQ-11.mol2 file you created above. You have to make them
exactly match, and the names are case-sensitive.
Also, study the leap.log file carefully: there should be other messages
pointing out the problem, especially if my diagnosis is correct.
....dac
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Received on Thu Jul 22 2010 - 06:00:07 PDT
