What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
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ther posts are usually solved by closely reading the text of the tutorial,
> not only the commands.
>
> Cheers,
>
> Tsjerk
>
>
> On Sun, Aug 25, 2013 at 3:44 AM, The One And Only >wrote:
>
> > Never mind, I'm dumb. I just realized that protein.pdb means i h
1xys.top Consequently, I
> don't think the ions are written into your .top . Please check and see if
> grompp works.
>
>
> On Sun, Aug 25, 2013 at 9:34 AM, The One And Only >wrote:
>
> > I've tried the same process twice to two different proteins, but still
I've tried the same process twice to two different proteins, but still got
the same error that the #coordinates in the topology file did not match the
#coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is
the process I went through:
*pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -
I've been able to set up everything correctly according to the tutorial I
found on the website. I got the following error when I typed:
grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o
1qlz-EM-solvated.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I
Never mind, I'm dumb. I just realized that protein.pdb means i have to
specify which protein i want like "1qlz.pdb" and not actually type
"protein.pdb" BUT THANKS GUYS!!
On Sat, Aug 24, 2013 at 6:40 PM, The One And Only wrote:
> so how do i solve the protein.pdb
so how do i solve the protein.pdb issue?
On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul wrote:
>
>
> On 8/24/13 9:26 PM, The One And Only wrote:
>
>> that's something i know nothing about; I just graduated from high school
>> and I have no background or experien
d to learn a bit about unix filesystems
>
>
> On Sat, Aug 24, 2013 at 6:18 PM, The One And Only >wrote:
>
> > So I started following some tutorials online since I didn't get a
> response
> > last time. the tutorial I'm using is:
> > http://nmr.chem.uu.nl
So I started following some tutorials online since I didn't get a response
last time. the tutorial I'm using is:
http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
I followed that tutorial to the second page and got stuck at the step where
it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p
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