Hi, Daniel was right. The AmberTools14 version I used was before update2 so
it truncated all my coordinates without displaying any error. This happened
because I hadn't a Internet connection during the compiling. I updated the
version and there are no problems. Thanks a lot, best regards
On Fri, Oct 17, 2014 at 2:01 PM, Francesco Gentile <fgentile.ualberta.ca>
wrote:
> 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
>>
>>
--
Francesco Gentile
PhD Student, Biophysics
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 Tue Oct 21 2014 - 13:30:05 PDT
