<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 31/03/2012 1:00 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopyhistoj_usg9iJvdJkNYJL-ivwnoBotZGKfnWP9XAQ+Q@mail.gmail.com"
type="cite">Mark,<br>
<br>
<br>
Also I'd like to know some more about most correct parametrisation
of such new edited system. My new system consist of two proteins (
one- wich was initially and the second small peptide wich I've
docked to the first protein). So now I need to define 2 separate
groups for the below enties of my MD files<br>
<br>
<font face="Arial"><font size="3"><code>energygrps = Protein
peptide<br>
</code></font></font>
<pre>tc-grps = Protein_Bilayer SOL_ions_peptide
and finally CoM groups because of the general anisotropy of the membrane system
comm-grps = Protein_Bilayer SOL_Ions_Peptide
I've made itp file for the peptide via pdb2gmx so in th default definition both the protein and peptide are the protein enty in the index file.
I've separate both of the protein and peptide by selection of two subsets of atoms wich represent to the each of that enties.
So finally I have two groups in the index.ndx file
a_1-5000 ( it's protein)
a_9999-10500 (it's peptide)
</pre>
</blockquote>
<br>
You can use make_ndx (or a text editor on the .ndx file) to give
them more helpful names.<br>
<br>
<blockquote
cite="mid:CAALQopyhistoj_usg9iJvdJkNYJL-ivwnoBotZGKfnWP9XAQ+Q@mail.gmail.com"
type="cite">
<pre>
Does this separation correct in general ? I have some fears because both protein and peptide consist of the same residue numbers in the GRO file ( e.g there are 212- lys wich is part of the protein and 212-Pro wich is part of the peptide ) Might this system be tended to errors?
</pre>
</blockquote>
<br>
Residue numbers are largely irrelevant. pdb2gmx and maybe grompp use
them for matching a coordinate file to the .rtp and .top
(respectively), but only really in the sense that the number changes
from one residue to another.<br>
<br>
<blockquote
cite="mid:CAALQopyhistoj_usg9iJvdJkNYJL-ivwnoBotZGKfnWP9XAQ+Q@mail.gmail.com"
type="cite">
<pre>
I have no errors during processing of that sustem by grompp as well as md run. What should I do for such system consisted of two proteins in separate phases ( membrane-like and water)
?
</pre>
</blockquote>
<br>
All seems basically sound.<br>
<br>
Mark<br>
</body>
</html>