[gmx-users] acetonitrile from amber to gromacs

[durmaz at zib.de]

thanks to all so far

@anthony
i have amberTools, but not the amber MD package. is that enough for my
purpose?

@rui
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
>>
>> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
>>
>> i found a gorgeous little box containing a pretty number of 6-site
>> modeled AN molecules, represented by 3 files:
>>
>> ch3cn_210.pdb
>> frcmod.ch3cn
>> prep.ch3cn
>>
>> 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!
>>
>> regards,
>>
>> vedat
>>
>>
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