I have AmberTools14, not sure if the new update. I will recompile as soon
as I will be in my lab. I will let you known about the result. Thanks so
much for your help, best regards
Francesco Gentile
On 17 Oct 2014 13:23, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> What version of AmberTools are you using? This problem sounds a lot
> like what was fixed with AmberTools 14 update 2 (truncated coordinate
> files). Make sure you are running the latest version. You can re-run
> configure to get the updates, then re-compile.
>
> Hope this helps,
>
> -Dan
>
> On Thu, Oct 16, 2014 at 3:36 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > You said:
> >
> >> when I tried to obtain the inpcrd file for the drug alone, it was empty
> >
> > so I guess I'm not sure what exactly the issue is. If you cannot
> > visualize the topology/restart in VMD then certainly something is
> > wrong. I think at this point we would need to see your exact workflow
> > (i.e. flags given to antechamber and commands given to tleap) to try
> > and help further. If you can provide me off-list with the problematic
> > topology/restart I may be able to debug a bit more.
> >
> > -Dan
> >
> >
> > On Thu, Oct 16, 2014 at 3:06 PM, Francesco Gentile <fgentile.ualberta.ca>
> wrote:
> >> 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
> >> _______________________________________________
> >> 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)
>
>
>
> --
> -------------------------
> 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
>
>
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Received on Fri Oct 17 2014 - 13:30:02 PDT
