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<pre wrap=""><div class="moz-txt-sig"><div class="moz-txt-sig">--__--__--
Message: 7
Subject: Re: [gmx-users] Help: No default LJ-14...
From: David van der Spoel <a class="moz-txt-link-rfc2396E"
href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a>
To: <a class="moz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
Organization:
Date: 20 Nov 2003 09:07:41 +0100
Reply-To: <a class="moz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
On Thu, 2003-11-20 at 09:00, Henrik Rundgren wrote:
</div></div></pre>
<blockquote type="cite">
<pre wrap=""><span class="moz-txt-citetags">> </span>hello all.
<span class="moz-txt-citetags">> </span>I have a problem.
<span class="moz-txt-citetags">> </span>I have run some simulations with Gromacs, and all seems fine.
<span class="moz-txt-citetags">> </span>No I try to run a small peptide in wter, and I get the following warnings:
<span class="moz-txt-citetags">> </span>
<span class="moz-txt-citetags">> </span> Generated 1179 of the 1378 non-bonded parameter combinations
<span class="moz-txt-citetags">> </span>WARNING 1 [file "top.top", line 86]:
<span class="moz-txt-citetags">> </span> No default LJ-14 types, using zeroes
<span class="moz-txt-citetags">> </span>WARNING 2 [file "top.top", line 87]:
<span class="moz-txt-citetags">> </span> No default LJ-14 types, using zeroes
<span class="moz-txt-citetags">> </span>WARNING 3 [file "top.top", line 88]:
<span class="moz-txt-citetags">> </span> No default LJ-14 types, using zeroes
<span class="moz-txt-citetags">> </span>WARNING 4 [file "top.top", line 109]:
<span class="moz-txt-citetags">> </span> No default LJ-14 types, using zeroes
<span class="moz-txt-citetags">> </span>WARNING 5 [file "top.top", line 110]:
<span class="moz-txt-citetags">> </span> No default LJ-14 types, using zeroes
<span class="moz-txt-citetags">> </span>WARNING 6 [file "top.top", line 111]:
<span class="moz-txt-citetags">> </span> No default LJ-14 types, using zeroes
<span class="moz-txt-citetags">> </span>Excluding 3 bonded neighbours for Protein 1
<span class="moz-txt-citetags">> </span>Excluding 2 bonded neighbours for SOL 884
<span class="moz-txt-citetags">> </span>
<span class="moz-txt-citetags">> </span>Then it continues and makes the infile .trp, but I doubt that this is ok
<span class="moz-txt-citetags">> </span>to run an simulation on....
<span class="moz-txt-citetags">> </span>I have checked in the topology file, and the default type value is 1
<span class="moz-txt-citetags">> </span>(=LJ)... so I don't see where this warning is coming from.
<span class="moz-txt-citetags">> </span><!---->
have you checked which atom pair is listed in top.top lines 86, 87, 88,
109-111
</pre>
<blockquote type="cite">
<pre wrap=""><span class="moz-txt-citetags">> </span>thanks for the help.
<span class="moz-txt-citetags">> </span>sincerely,
<span class="moz-txt-citetags">> </span>henrik
</pre>
</blockquote>
<!---->
<div class="moz-txt-sig">-- David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3,
Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511
755 <a class="moz-txt-link-abbreviated"
href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a
class="moz-txt-link-abbreviated" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a
class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/%7Espoel">http://xray.bmc.uu.se/~spoel</a>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ </div>
<pre wrap=""></pre>
</blockquote>
<pre wrap=""><!---->
</pre>
<br>
Hello,<br>
Yes, I have looked in it.. but I can't understand why it would want to
use the ZN: or SI: or <a class="moz-txt-link-freetext" href="NA:pairs">NA:pairs</a> in the topology file... since I haven't
defined any "metals" in the pdb file (it's just a basic dipeptide of
ALA ZW-form). <br>
I have missed some basics here... shouldn't the topology only include
the atoms defined from the pdb file's?<br>
(I used your spc216 file for water though. but that one seems ok when
looking at it...)<br>
<br>
From top.top following can be read...<br>
<br>
[ nonbond_params ]<br>
line ; i j func c6 c12<br>
86 O NL 1 0.23473E-02 0.34518E-05<br>
87 O NR5* 1 0.23473E-02 0.20711E-05<br>
88 O ZN 1 0.00000E+00 0.10931E-06<br>
109 OM NR6* 1 0.23473E-02 0.33890E-05<br>
110 OM SI 1 0.57734E-02 0.86722E-05<br>
111 OM NA 1 0.40370E-03 0.44478E-06<br>
<br>
thanks for input.<br>
henrik<br>
<pre class="moz-signature" cols="72">--
_________________________________________________________________
Henrik Rundgren
Division of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm
Sweden
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Henrik@physc.su.se">Henrik@physc.su.se</a>
Telephone: +46-(0)8-16 12 63
Fax: +46-(0)8-15 21 87
Website: <a class="moz-txt-link-abbreviated" href="http://www.fos.su.se/~henrik">www.fos.su.se/~henrik</a>
_________________________________________________________________
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