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)
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Received on Thu Oct 16 2014 - 15:00:02 PDT
