Hi Niyaz,
The author of the package will have the best answers to these questions.
But you should be able to find in the source files where the mdp file is
written. There you can make changes, to make sure that coulombtype is set
to PME and tcoupltype is set to v-rescale. In addition, you probably
Dear, PyMol-Gromacs experts,
I used to use PyMol Dynamics plugin to make some MDs.
It makes me more than sad I always get notes like:
-
NOTE 1 [file em.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider usin
I encounter the following error when starting pymol on a laptop, and as a
result, pymol crashes.
can anyone help me to resolve this issue?
This Executable Build integrates and extends Open-Source PyMOL 1.7.2.1.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version
I am sorry that I forgot to mention, the reason why I cannot make movie
with more frames is that I am working on a morph from an external. That
software has a maximum number of frames to output.
Thank you,
Chen
On Fri, Sep 12, 2014 at 4:19 PM, Chen Zhao wrote:
> Dear all,
>
> I am now having a
Dear all,
I am now having a problem of changing the frame rate when saving the movie.
Even if I set the frame rate by "Movie->frame rate", the frame rate will
stay at the default value if I save the movie as MPEG file. I know there is
another way to do this, in which I save all the frames as png f
> csplit -b "%03d.pdb" test.pdbqt /^MODEL/ {0} > somelog.log
>
man csplit:
csplit -f blabla -b "%03d.pdb" test.pdbqt /^MODEL/ {1}
But you want only the first frame anyway, so no real use for csplit...
sed /^ENDMDL/q my_docking.pdb | grep -v "^ROOT\|^ENDROOT\|^TORSDOF
> 0\|^MODEL\|^REMARK" | se
Hi Tsjerk,
many thanks for the suggestions
in my case
csplit -b "%03d.pdb" test.pdbqt /^MODEL/ {0} > somelog.log
is not good because in always produces 000.pdb which is the empty file.
Also I dont know why but all files also consist of the xx prefix (e.g
xx000.pdb xx005.pdb etc).
so in my case be
Thank you very much!
James
2014-09-12 12:36 GMT+02:00 Marko Hyvonen :
> On 12/09/2014 11:26, James Starlight wrote:
>
>> grep -v "^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK"|
>>
>
> I think you are missing few "|" in there:
>
> grep -v "^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK"
>
> and depen
Hi Marko,
in my case
this (long ) is works fine
gleb@gpu2:~/Documents/script/docking/Complex/OR1A1_MULTI> cat receptor.pdb
xx001.pdb | grep -v '^ROOT'| grep -v '^ENDROOT' | grep -v '^TORSDOF 0' |
grep -v '^MODEL' | grep -v '^REMARK' | sed -e 's/^ENDMDL/TER/g' >
complex.pdb
but in the below c
Hi James,
How about
egrep -v "MODEL 1|ROOT|ATOMS|ENDROOT|TORSDOF" myoriginalfile | sed
's/ENDMDL/TER/' > mynewfile
-v in egrep is to reverse the selection so you get all lines except that
ones in the expression. Without that you _only_ "grep" the lines with
those expressions.
(egrep might be
Hi James,
This is more text-file processing than it is bioinformatics. The trick is
to understand the problem, dissect it, and fit it to your toolbox on Linux.
That's actually much of bioinformatics :)
The first thing to understand is what data you have and what data you need
to have in the end.
Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)
because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands
e
Hi James,
These are the sort of questions that'll be answered elsewhere. Most notably
on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b "%04d.pdb" file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, Ja
Hi,
some new question.
I need to some combination of shell utilities to split multi_model.pdb on
several pdbs as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb > model1.pdb
bu
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