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
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--
-------------------------
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)
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Received on Thu Oct 16 2014 - 13:00:02 PDT
