[gmx-users] acetonitrile from amber to gromacs
durmaz at zib.de
durmaz at zib.de
Wed May 19 20:33:13 CEST 2010
thanks to all so far
i have amberTools, but not the amber MD package. is that enough for my
acpypi -i ch3cn_210.pdb
says: "cannot find template for residue C3N in our library". and indeed,
there's no residue C3N in my ffamber99sb.rtp file
(and i don't know, how to use it in order to generate my topology or even
an rtp file?!)
but (@vitaly) editconf does create the gro file which is fine.
however, when i use
x2top -f ch3cn_210.pdb -ff select -r x2top.rtp
and choose ffamber99sb as force field, i get the error message
"Library file ffamber99sb.n2t not found in current dir nor in your GMXLIB
path". there are n2t files, but not for the amber ff.
what have i done wrong?
> I did it for other solvent. If you have AMBER is very easy to do. Do
> you have AMBER?
> On Wed, May 19, 2010 at 12:15 PM, vedat durmaz <durmaz at zib.de> wrote:
>> hi all together,
>> this week i'm trying to do some simulations with acetonitrile (AN) as a
>> solvent and using ffamber99 as force field. on this website
>> i found a gorgeous little box containing a pretty number of 6-site
>> modeled AN molecules, represented by 3 files:
>> does anyone have an idea, how to generate .gro/.itp files out of these
>> amber files, preferably by pushing a single button of some proper tool??
>> i'ld be the happiest guy in world if someone told me the trick!
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