<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 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 4:27 PM, tarak karmakar wrote:
<blockquote type="cite"><font size="4">Dear All,<br>
<br>
<br>
In my protein pdb file I have changed some of the amino
acid residue names. So accordingly I have changed corresponding
residue names in force filed files and kept all the files [
modified and unmodified ] in my current working directory. Those
files are <br>
<br>
1) atomtypes.atp<br>
2) aminoacids.rtp<br>
3) ffnonbonded.itp<br>
4) ffbonded.itp<br>
5) spc.itp<br>
6) ions.itp<br>
<br>
now while giving the command <br>
pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top <br>
<br>
how can I make use of all these force field files present in my
current working directory ?</font><br>
</blockquote>
<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 class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
</font></span></div>
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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>