Dear Vedat,<div><br></div><div>Thank you very much indeed. Things only get better with constructive feedbacks, either positive or negative.</div><div><br></div><div>Glad you're managing well your problem. However, as I see, your problem now is in the tleap level.</div>
<div><br></div><div>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).</div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div><div>I hope it helps.</div><div><br></div>
<div>Best,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">On Fri, Jun 4, 2010 at 11:00, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div id=":vm" class="ii gt">hi alan and all others,<br>
<br>
i love it. i've probably never seen such a helpful and constuctive<br>
answer to a question asked over the gmx user mailing list. following<br>
your instructions was very informative on the one hand and provided the<br>
results that i needed on the other.<br>
<br>
slightly modifying the the ch3cn.frcmod and -.prep files from the<br>
manchester site in accordance with a newer solvent model for<br>
acetonitrile of the year 2007 and feeding tleap with that data resulted<br>
in a ch3cn.lib file and afterwards in ch3cn.prmtop and ch3cn.inpcrd<br>
which i could use as input for acpype in order to generate .gro and .itp<br>
files. perfect.<br>
<br>
almost perfect, because in tleap i was not able to add the YC-YN triple<br>
bond (with the "bond ..." command) without generating an error message<br>
when saving my parameter files ("saveAmberParm ..." command). see the<br>
following output:<br>
<br>
<br>
> bond C3N.1.C2 C3N.1.N1 "T"<br>
> saveAmberParm C3N ch3cn.prmtop ch3cn.inpcrd<br>
Checking Unit.<br>
Building topology.<br>
Building atom parameters.<br>
Building bond parameters.<br>
Building angle parameters.<br>
Building proper torsion parameters.<br>
!FATAL ERROR----------------------------------------<br>
!FATAL: Â Â In file [unitio.c], line 1778<br>
!FATAL: Â Â Message: 1-4: cannot add bond 1 2<br>
This may be caused by duplicate bond specifications;<br>
for example, explicit bond commands in addition to PDB conect records.<br>
!<br>
!ABORTING.<br>
<br>
where could the "second" bond specification be, that avoids the<br>
specification of a triple bond "T"? there's no bonding information in<br>
the pdb file.<br>
<br>
a step earlier in tleap, i had to addAtomTypes YN and YC, however, there<br>
was no way to specify them with "sp" hybridization, but "sp2" resulting<br>
in two lines each containing a single bond between these two atoms<br>
within the "!entry.C3N.unit.connectivity table" section of the ch3cn.lib<br>
file (seems to be a double bond).<br>
<br>
is this issue negligible, since the force constants and equilibrium<br>
angles (180 degrees) are already describing the right molecule?<br>
<br>
vedat<br>
<br>
<br>
<br>
<br>
Alan schrieb:<br>
> Nice, glad you did progress. See below.<br>
><br>
> On Thu, May 20, 2010 at 12:38, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>> wrote:<br>
><br>
> Â Â thanks for your helpful hints. i updated acpype, created a pdb<br>
> Â Â file with<br>
> Â Â a single molecule and ran<br>
><br>
> Â Â acpype -i ch3cn_210_single.pdb<br>
><br>
> Â Â which generated an .itp and other interesting files. that's<br>
> Â Â nice. (remember, i want to use gromacs with amber99sb force field<br>
> Â Â and i<br>
> Â Â downloaded 3 files from the amber site: ch3cn_210.pdb,<br>
> Â Â frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)<br>
><br>
> Â Â 1) the charges do not match the ones listed in the prep.ch3cn file.<br>
> Â Â shall i just change them by hand accordingly?<br>
><br>
><br>
> It doesn't match because it's using am1bcc, which was parametrised to<br>
> reproduce the RESP charges, but obviously (sqm is semi-empirical<br>
> method, not like gaussian) Â it won't be accurate.<br>
><br>
> However, you're right, if you have the RESP charges in prep.ch3cn just<br>
> copy them by hand accordingly.<br>
><br>
> Or even better, if you want to learn more about the whole stuff,<br>
> double check if the parameters you got from the Manchester site are<br>
> OK, why not trying <a href="http://q4md-forcefieldtools.org/RED/" target="_blank">q4md-forcefieldtools.org/RED/</a><br>
> <<a href="http://q4md-forcefieldtools.org/RED/" target="_blank">http://q4md-forcefieldtools.org/RED/</a>>? Once you got the charges (they<br>
> should be very close if not the same from  prep.ch3cn), you can use<br>
> acpype just to generate the topology by providing a c3n.MOL2 file with<br>
> the charges calculated by RED and then using "acpype -di c3n.mol2 -c<br>
> user".<br>
><br>
><br>
> Â Â 2) dummy atoms as listed in the prep.ch3cn are not present in the new<br>
> Â Â .itp file.<br>
><br>
><br>
> I guess you don't know how a prep file works, so<br>
> see <a href="http://ambermd.org/doc/prep.html" target="_blank">http://ambermd.org/doc/prep.html</a>.<br>
><br>
><br>
> Â Â 3) the force constants seem totally different. shall i again just<br>
> Â Â adjust<br>
> Â Â them to the original file obtained from the amber site?<br>
><br>
><br>
> If using acpype with default mode, so you'd get GAFF parameters. You<br>
> may want to try:<br>
><br>
> acpype -di c3n.mol2 -c user -a amber<br>
><br>
> However, it still may diff. If you read Jaime's paper and you agree<br>
> with what he did, so you can "copy&paste" his parameters as well.<br>
><br>
><br>
> Â Â is there another way of using acpype, with a proper args list, that i<br>
> Â Â should use in this situation?<br>
><br>
><br>
> Read the Wikis in the acpype site and 'acpype -h'. I am always keen<br>
> for suggestions.<br>
><br>
> Another possible way, would be using tleap from AmberTools, generate<br>
> just one molecule, save parameters and use acpype to convert from<br>
> amber to gromacs, something like<br>
><br>
> acpype -p c3n.prmtop -x c3n.inpcrd<br>
><br>
> If doing so, you'd get the exactly Jaime's topology but in gromacs<br>
> format (gro and top file, not itp, so you may need to adjust things in<br>
> the top file in order to create a itp, but should be a simple task).<br>
><br>
> Â Â > BTW, how did you get this message "cannot find template for residue<br>
> Â Â > C3N in our library"?<br>
> Â Â i got that message *within* the following output when running:<br>
> Â Â >acpype -i ch3cn_210.pdb<br>
> Â Â [...]<br>
> Â Â Warning: cannot find template for residue C3N in our library.<br>
> Â Â Â Â Â Â You will not be able to save prmtop for this molecule.<br>
> Â Â Warning: cannot find template for residue C3N in our library.<br>
> Â Â Â Â Â Â You will not be able to save prmtop for this molecule.<br>
> Â Â [gtkleap]$ #check C3N<br>
> Â Â [gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd<br>
> Â Â Error: dparm pchg does not exist!<br>
><br>
> Â Â ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
> Â Â ERROR: Sleap failed<br>
> Â Â ==> Removing temporary files...<br>
> Â Â ACPYPE FAILED: [Errno 2] No such file or directory:<br>
> Â Â 'ch3cn_210_AC.inpcrd'<br>
> Â Â Total time of execution: 7s<br>
><br>
><br>
> Ah, ok, I should've know this... It's a fall back routine to try to<br>
> use 'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately.<br>
><br>
> Thanks for trying acpype.<br>
><br>
> Cheers,<br>
><br>
> Alan<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>