Thanks a lot........now it's working....:)<br><br><div class="gmail_quote">On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham <span dir="ltr"><<a 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">
On 15/06/2012 6:21 PM, tarak karmakar wrote:
</div><blockquote type="cite"><div class="im"><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><div class="gmail_quote"><div class="im">
On Fri, Jun 15, 2012 at 12:50 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
</div><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> <br>
</div>
You need the kind of approach described here <a 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><font color="#888888"><br>
</font></span><br>
</div>
</blockquote>
</div></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...<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
</font></span></div>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br><font size="4"><i style="font-family:times new roman,serif"><b>Tarak Karmakar<br>
Molecular Simulation Lab.<br>Chemistry and Physics of Materials Unit<br>Jawaharlal Nehru Centre for Advanced Scientific Research <br>Jakkur P. O. <br>Bangalore - 560 064<br>Karnataka, INDIA<br>Ph. (lab) : +91-80-22082809 </b></i></font><br>