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)
_______________________________________________
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Received on Fri Oct 17 2014 - 12:30:03 PDT
