VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Nov 25 2016 - 07:40:26 CST

Hi Sourav,

Your system seems to be missing the development files for Tcl. There should
be a package you can install named tcl-devel or something similar.

Best,
Jerome

On 25 November 2016 at 02:55, Sourav Ray <souravray90_at_gmail.com> wrote:

> Hello Jerome
>
> I am getting the error below while running the make:
>
> g++ -fpic -O3 -I/usr/include/tcl -c -o qwrap.o qwrap.cpp
> qwrap.cpp:1:17: fatal error: tcl.h: No such file or directory
> compilation terminated.
> <builtin>: recipe for target 'qwrap.o' failed
> make: *** [qwrap.o] Error 1
>
> And this one while running on Tcl:
>
> package require qwrap
> couldn't load file "qwrap.so": qwrap.so: cannot open shared object file:
> No such file or directory
>
> Please let me know how to fix it or I missed some step?
>
> Thanks and regards
> Sourav
>
> On Sat, Nov 19, 2016 at 11:46 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> Hi Norman and everyone,
>>
>> A quick unwrapping feature is now available as "qunwrap".
>> https://github.com/jhenin/qwrap
>>
>> Please give it a spin and let me know what you think!
>>
>> Jerome
>>
>> On 17 November 2016 at 10:09, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>>
>>> Hi Norman,
>>>
>>> You are not the only one to request such a feature. I'm definitely going
>>> to implement that, but not as "remove long bonds", which is cumbersome and
>>> is done by "pbc join" in PBCTools, but rather what I implemented in "pbc
>>> unwrap", that is, remove large jumps from one frame to the next. That
>>> requires a more or less continuous trajectory starting from a "clean"
>>> configuration where all the fragments are in one piece.
>>>
>>> Jerome
>>>
>>>
>>>
>>> On 17 November 2016 at 09:05, Norman Geist <
>>> norman.geist_at_uni-greifswald.de> wrote:
>>>
>>>> Hey,
>>>>
>>>>
>>>>
>>>> thanks for your work so far. Would it be difficult to also implement a
>>>> unwrap function (more or less remove long bonds)? Since f.i. GROMACS
>>>> outputs trajectories always wrapped.
>>>>
>>>>
>>>>
>>>> Norman
>>>>
>>>>
>>>>
>>>> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
>>>> Auftrag von *Jérôme Hénin
>>>> *Gesendet:* Mittwoch, 16. November 2016 14:55
>>>> *An:* VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>>> *Betreff:* vmd-l: Fast PBC wrapping in VMD
>>>>
>>>>
>>>>
>>>> Hi everyone,
>>>>
>>>>
>>>>
>>>> This is a reminder that there is a faster alternative to pbc wrap from
>>>> the PBCTools plugin, in the form of qwrap:
>>>>
>>>> https://github.com/jhenin/qwrap
>>>>
>>>>
>>>>
>>>> It has improved since the last time I mentioned it on this list,
>>>> specifically, you can now restrict the wrapping to a given selection, as in
>>>> (my personal favorite):
>>>>
>>>> qwrap sel "not protein" center protein
>>>>
>>>>
>>>>
>>>> Thanks to a contribution by Giacomo Fiorin, wrapping can also be done
>>>> based on VMD fragments.
>>>>
>>>>
>>>>
>>>> Qwrap is written in C and is relatively simple-minded, hence the speed--001a114dd4ccf6b80605422044b4--