I fixed it ... but now after using the command : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr <br><br>I am getting a charge of -9.999971e-01<br><br><br>Since the charge has to be in whole number, what shall I do in this case. (The ligand that I am using is phosphotyrosine)<br>
<br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">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 class="im">On 21/06/2011 3:03 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Now I changed the .top file in this way and I am getting this error now :-<br>
<br>
change :- ; Include forcefield parameters<br>
#include "charmm27.ff/forcefield.itp"<br>
<br>
;Include ligand topology<br>
#include "PTR.itp"<br>
<br>
[ moleculetype ]<br>
; Name nrexcl<br>
Protein_chain_A 3<br>
<br>
=====================<br>
<br>
error:-<br>
<br>
<br>
Ignoring obsolete mdp entry 'title'<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#<br>
Generated 23220 of the 23220 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 1<br>
Generated 20092 of the 23220 1-4 parameter combinations<br>
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>
<br>
------------------------------<u></u>-------------------------<br>
Program grompp, VERSION 4.5.4<br>
Source code file: toppush.c, line: 1987<br>
<br>
Fatal error:<br>
No such moleculetype LIG<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<br>
</blockquote>
<br></div>
You have to make an attempt to solve your own problems :-) We have better things to do than oversee every move you make. Follow that link and read about this issue.<div><div></div><div class="h5"><br>
<br>
Mark<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>