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On 21/06/2011 4:15 PM, bharat gupta wrote:
<blockquote
cite="mid:BANLkTikapTChzZG4aFwbshEJOzG=kCbQHQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
OK, that's what I expected you were doing - truncating the output
and not rounding appropriately. See <a
href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a>
again - I've updated it to deal with this issue more explicitly.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikapTChzZG4aFwbshEJOzG=kCbQHQ@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Tue, Jun 21, 2011 at 2:13 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im">On 21/06/2011 3:03 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
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>
-------------------------------------------------------<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 moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<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 class="h5"><br>
<br>
Mark<br>
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</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 moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
<br>
</blockquote>
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