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

Alan alanwilter at gmail.com
Thu May 20 14:19:53 CEST 2010

Nice, glad you did progress. See below.

On Thu, May 20, 2010 at 12:38, <gmx-users-request at gromacs.org> wrote:

> 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?

It doesn't match because it's using am1bcc, which was parametrised to
reproduce the RESP charges, but obviously (sqm is semi-empirical method, not
like gaussian)  it won't be accurate.

However, you're right, if you have the RESP charges in prep.ch3cn just copy
them by hand accordingly.

Or even better, if you want to learn more about the whole stuff, double
check if the parameters you got from the Manchester site are OK, why not
trying q4md-forcefieldtools.org/RED/? Once you got the charges (they should
be very close if not the same from  prep.ch3cn), you can use acpype just to
generate the topology by providing a c3n.MOL2 file with the charges
calculated by RED and then using "acpype -di c3n.mol2 -c user".

> 2) dummy atoms as listed in the prep.ch3cn are not present in the new
> .itp file.

I guess you don't know how a prep file works, so see

>  3) the force constants seem totally different. shall i again just adjust
> them to the original file obtained from the amber site?

If using acpype with default mode, so you'd get GAFF parameters. You may
want to try:

acpype -di c3n.mol2 -c user -a amber

However, it still may diff. If you read Jaime's paper and you agree with
what he did, so you can "copy&paste" his parameters as well.

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

Read the Wikis in the acpype site and 'acpype -h'. I am always keen for

Another possible way, would be using tleap from AmberTools, generate just
one molecule, save parameters and use acpype to convert from amber to
gromacs, something like

acpype -p c3n.prmtop -x c3n.inpcrd

If doing so, you'd get the exactly Jaime's topology but in gromacs format
(gro and top file, not itp, so you may need to adjust things in the top file
in order to create a itp, but should be a simple task).

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

Ah, ok, I should've know this... It's a fall back routine to try to use
'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately.

Thanks for trying acpype.



Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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