[gmx-users] Re: acetonitrile from amber to gromacs

vedat durmaz durmaz at zib.de
Thu May 20 12:37:01 CEST 2010

Alan schrieb:
> Dear Vedat,
> On Wed, May 19, 2010 at 20:36, <gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> wrote:
>     @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?!)
> Have a bit of patience and try to read a bit more about ACPYPE.
> 1) Read the info there, I am sure you'll find it useful;
> 2) You'll learn that you need to have just one molecule in a pdb and
> not the whole box if you want the topologi of C3N.
> 3) It took me 2s to get the topology with acpype but months to write
> the code, so if you'd take some few minutes to read and use an updated
> version (it's not acpypi anymore BTW)...
thanks for your helpful hints. i updated acpype, created a pdb file with
a single molecule and ran

acpype -i ch3cn_210_single.pdb

which generated an .itp and other interesting files. that's
nice. (remember, i want to use gromacs with amber99sb force field and i
downloaded 3 files from the amber site: ch3cn_210.pdb,
frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)

1) the charges do not match the ones listed in the prep.ch3cn file.
shall i just change them by hand accordingly?
2) dummy atoms as listed in the prep.ch3cn are not present in the new
.itp file.
3) the force constants seem totally different. shall i again just adjust
them to the original file obtained from the amber site?

is there another way of using acpype, with a proper args list, that i
should use in this situation?

i know, that's many questions, but is has to be done!

> BTW, how did you get this message "cannot find template for residue
> C3N in our library"?
i got that message *within* the following output when running:
>acpype -i ch3cn_210.pdb
Warning: cannot find template for residue C3N in our library.
         You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue C3N in our library.
         You will not be able to save prmtop for this molecule.
[gtkleap]$ #check C3N
[gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd
Error: dparm pchg does not exist!

ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd'
Total time of execution: 7s

> acpype.googlecode.com <http://acpype.googlecode.com>
> Regards,
> Alan
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<

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