Dear Vedat,
Thank you very much indeed. Things only get better with constructive
feedbacks, either positive or negative.
Glad you're managing well your problem. However, as I see, your problem now
is in the tleap level.
So, are you in amber mailing list? If so I would suggest to post your
question there. If not, let me know and I try to post the question there
(you may want to consider joining it, very useful, even for those who uses
only ambertools).
However, at first, I would go ahead and neglect the error. In the end, if
you not happy, you can always adjust this particular parameter (in the itp
file), since in principle a triple bond would mean a stronger bond, so
implying in higher K-string constant. For how much to adjust? Well, you
cannot even ever say that you got is "correct"; all you can get is a better
or worse model and in the end it's up to you to set that.
Nevertheless, be sure that you have the right protonation state and try to
re-run your case putting CONECT info in the pdb just to check it.
I hope it helps.
Best,
Alan
On Fri, Jun 4, 2010 at 11:00, <gmx-users-requ...@gromacs.org> wrote:
> 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.
> !
> !ABORTING.
>
> 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?
>
> vedat
>
>
>
>
> Alan schrieb:
> > Nice, glad you did progress. See below.
> >
> > On Thu, May 20, 2010 at 12:38, <gmx-users-requ...@gromacs.org
> > <mailto:gmx-users-requ...@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<<
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