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On 15/06/2012 6:21 PM, tarak karmakar wrote:
<blockquote
cite="mid:CAGZMOosRjVj00yR2pwxBS6M6zOrYKPeKqxTQ1_M01jxGDuvptQ@mail.gmail.com"
type="cite"><font size="4">Hi, <br>
<br>
Thanks for the reply. <br>
One thing, while giving the '-ff' flag it is asking for some
string. So I renamed all my force field files as except spc.itp
and ions.itp. Renamed files are .....<br>
<br>
1) ffprot.atp<br>
2) ffprot.rtp<br>
3) ffprot.itp [ includes ffnonbonded.itp and ffbonded.itp ]<br>
<br style="color:rgb(255,0,0)">
<span style="color:rgb(255,0,0)">pdb2gmx -f test.pdb -o test.gro
-p toplo.top -ff prot <br>
<br>
</span>so it'll read all of these files starting with 'ff'<br>
Then how can I deal with spc.itp and ions.itp files ?? Should I
include the scp.itp and ions.itp files inside the ffprot,itp ??</font><br>
<br>
<div class="gmail_quote">
On Fri, Jun 15, 2012 at 12:50 PM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> <br>
</div>
You need the kind of approach described here <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><span
class="HOEnZb"><font color="#888888"><br>
</font></span><br>
</div>
</blockquote>
</div>
</blockquote>
<br>
You started with files from some force field. Copy the whole folder,
like it says in the above link. Then modify the files there...<br>
<br>
Mark<br>
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