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

vedat durmaz durmaz at zib.de
Fri Jun 4 11:17:11 CEST 2010

hi alan and all others,

i love it. i've probably never seen such a helpful and constuctive
answer to a question asked over the gmx user mailing list. following
your instructions was very informative on the one hand and provided the
results that i needed on the other.

slightly modifying the the ch3cn.frcmod and -.prep files from the
manchester site in accordance with a newer solvent model for
acetonitrile of the year 2007 and feeding tleap with that data resulted
in a ch3cn.lib file and afterwards in ch3cn.prmtop and ch3cn.inpcrd
which i could use as input for acpype in order to generate .gro and .itp
files. perfect.

almost perfect, because in tleap i was not able to add the YC-YN triple
bond (with the "bond ..." command) without generating an error message
when saving my parameter files ("saveAmberParm ..." command). see the
following output:

> bond C3N.1.C2 C3N.1.N1 "T"
> saveAmberParm C3N ch3cn.prmtop ch3cn.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL:    In file [unitio.c], line 1778
!FATAL:    Message: 1-4: cannot add bond 1 2
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.

where could the "second" bond specification be, that avoids the
specification of a triple bond "T"? there's no bonding information in
the pdb file.

a step earlier in tleap, i had to addAtomTypes YN and YC, however, there
was no way to specify them with "sp" hybridization, but "sp2" resulting
in two lines each containing a single bond between these two atoms
within the "!entry.C3N.unit.connectivity table" section of the ch3cn.lib
file (seems to be a double bond).

is this issue negligible, since the force constants and equilibrium
angles (180 degrees) are already describing the right molecule?


Alan schrieb:
> Nice, glad you did progress. See below.
> On Thu, May 20, 2010 at 12:38, <gmx-users-request at gromacs.org
> <mailto: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/
> <http://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 http://ambermd.org/doc/prep.html.
>     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 suggestions.
> 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.
> Cheers,
> 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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