Hi, thanks for the fast reply. I cannot find any error in leap.log file,
just some warnings about close contacts of atoms(that is normal, I found
the same warnings in the other complexes). The inpcrd files for the complex
and the molecule are not blank, they just don't work without showing any
error in tleap. The fact that there are no errors displayed in the log file
but the file is not useful for simulations sounds to me very weird, as the
prmtop file contains also the informations about the small molecule; I
cannot find any reason for that. I'm actually trying to rebuild the
molecule from the beginning and re dock it, then I will try to simulate
again the complex.
On Thu, Oct 16, 2014 at 1:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Oct 16, 2014 at 11:55 AM, Francesco Gentile
> <fgentile.ualberta.ca> wrote:
> > moreover when I try to load the topology and the coordinates files in VMD
> > nothing is appearing on the screen (I selected amber 7 parm for prmtop
> file
> > and amber 7 restart for the inpcrd) . There are not errors displayed by
>
> If your input coordinates are blank you need to figure out why they
> are not being written by tleap. When you perform your 'saveamberparm'
> command pay close attention to the output - are any warnings/errors
> listed there? Obtaining just a PDB isn't a good test here because
> 'saveamberparm' is a bit more "strict" in the sense that more
> error-checking is performed.
>
> > antechamber or VMD, and when I tried to obtain the inpcrd file for the
> drug
> > alone, it was empty (while the prmtop file was ok). However the pdb
> > obtained with tleap for the same complex works perfectly on VMD. I tried
> > also to obtain a rst file from this pdb using VMD and use it together
> with
>
> The Amber restart-writing capability of VMD has been broken for as
> long as I can remember. At any rate, you're better off trying to
> figure out what went wrong prior to this rather than use this as a
> workaround.
>
> -Dan
>
> > the prmtop for my simulations instead of the inpcrd but it gives me the
> > following error again in the output file:
> >
> > | ERROR: nfft1 must be in the range of 6 to 512!
> > | ERROR: nfft3 must be in the range of 6 to 512!
> > | ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
> > | ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
> > | ERROR: alpha must be in the range of 0.30000E+02 to 0.15000E+03!
> > | ERROR: beta must be in the range of 0.30000E+02 to 0.15000E+03!
> > | ERROR: gamma must be in the range of 0.30000E+02 to 0.15000E+03!
> >
> > Input errors occurred. Terminating execution.
> >
> > I don't know what I'm doing wrong as the scripts that I'm using for
> > preparing and simulating my complex are the same I used for the other
> > complexes (that were already prepared and simulated without any problem).
> > I'm guessing that there is something wrong with the small molecule but
> as I
> > said before no errors were displayed during the preparation phase and the
> > structure looks ok. I already tried to rebuild the drug and re dock it in
> > Autodock, but nothing is changed. I really appreciate if someone could
> help
> > me with this issue. Many thanks, best regards
> >
> > Francesco Gentile
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Francesco Gentile
PhD Candidate, Biophisycs
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
Canada
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Received on Thu Oct 16 2014 - 14:30:02 PDT
