Hi Xiaodu,<br><br>Yes I remember now I had the same problem. Copy the forcefield.itp to your working directory and make the change there. Your working directory is searched first. However as you will be including a protein in your simulation you will need to have fudge set to 0.5 for 1-4 scaling with the AMBER forcefield... <br>
Personally I would look into doing mixed scaling with gromacs. This is how it is done in amber (the software package) when mixing these two forcefields but I can't help you here with gromacs, but I believe from reading the AMBER mailing list archive it is possible to scale on a per molecule basis. <br>
<br>
<a href="http://dev-archive.ambermd.org/200812/0000.html">http://dev-archive.ambermd.org/200812/0000.html</a><br><br>Here is the relevant part of the thread:<br><br>Hi Rob,
<br>
It was great to see you yesterday at the glycan array workshop. I'm
<br>
here with Erik Lindahl, and we're chatting about implementing mixed
<br>
1-4 scaling in gromacs. It's easy to enable on a per-molecule basis.
<br>
Enabling on a per-residue and per-atom basis is certainly possible,
<br>
but there are a bunch of ways to do it. Do you have a sense of how
<br>
you'd like to see this done? One idea would be to enable two
<br>
different 1-4 pair types, one with default 1-4 scaling and one with
<br>
user-specified scaling. And how should the interface be handled? I
<br>
assume that it goes to default at that point (we want the protein 1-4
<br>
scaling at the NLN).
<br>
<br>
Best wishes,
<br>
--Peter
<br><br>
<br><div class="gmail_quote">2010/12/27 gromacs564 <span dir="ltr"><<a href="mailto:gromacs564@126.com" target="_blank">gromacs564@126.com</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<pre>Hi <span style="line-height: 25px;">Oliver</span></pre><pre><span style="line-height: 25px;">I'm sorry to reply you so later.And </span><span style="line-height: 25px;">I have some questions after reading your letter.</span></pre>
<pre><span style="line-height: 25px;">You said that “</span><span style="line-height: 25px;">The fudgeLJ under defaults should be 1.0 for GLYCAM“ and ”</span><span style="line-height: 25px;">When you run grompp check in the</span></pre>
<span style="line-height: 25px;"><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif; font-size: 14px; line-height: 25px; padding: 8px 10px; margin: 0px;">output that fudge is set to 1.0.” Do you means to setting the fudgeLJ value to 1.0 in em.tpr file？I am not sure.</pre>
<pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif; font-size: 14px; line-height: 25px; padding: 8px 10px; margin: 0px;">I want to change this gromacs top files( all the output files by <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> converted) to gromacs itp files,then included in protein top file. And I plan to use the amber03 force filed. But I think that the "[ defaults ]" cannot included in itp files,or will cause an error about redifiniton.Because the "[ defaults ]" had exist in ”forcefield.itp".</pre>
<pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif; font-size: 14px; line-height: 25px; padding: 8px 10px; margin: 0px;">------------------------------------------------------------------------------------------</pre>
</span><pre><span style="line-height: 25px;">;myt.itp
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5（ =1.0 ? ） 0.8333</span></pre><pre><span style="line-height: 25px;">------------------------------------------------------------------------------------------------</span></pre>
<pre><span style="line-height: 25px;">#define _FF_AMBER
#define _FF_AMBER03
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333</span></pre><pre><span style="line-height: 25px;">----------------------------------------------------------------------------------------------------------</span></pre>
<pre><span style="line-height: 25px;"> </span><span style="line-height: 25px;">So，do you know how to slove this problem？Can you give me some suggestion or a correct copy file by </span></pre><pre><span style="line-height: 25px;"></span><span style="line-height: 25px;"> <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> converted? Thank you very much.</span></pre>
<span style="line-height: 25px;"><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif; font-size: 14px; line-height: 25px; padding: 8px 10px; margin: 0px;">My email address：<a href="mailto:gromacs564@126.com" target="_blank">gromacs564@126.com</a></pre>
<pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif; font-size: 14px; line-height: 25px; padding: 8px 10px; margin: 0px;">xiaodu</pre></span><pre><span style="line-height: 25px; white-space: normal;"><pre style="white-space: pre-wrap; word-wrap: break-word; font-size: 14px; font-family: arial,verdana,sans-serif; line-height: 25px; padding: 8px 10px; margin: 0px;">
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