<pre>Hi <span class="Apple-style-span" style="line-height: 25px; ">Oliver</span></pre><pre><span class="Apple-style-span" style="line-height: 25px;">I'm sorry to reply you so later.And </span><span class="Apple-style-span" style="line-height: 25px; ">I have some questions after reading your letter.</span></pre><pre><span class="Apple-style-span" style="line-height: 25px; ">You said that ¡°</span><span class="Apple-style-span" style="line-height: 25px; ">The fudgeLJ under defaults should be 1.0 for GLYCAM¡° and ¡±</span><span class="Apple-style-span" style="line-height: 25px; ">When you run grompp check in the</span></pre><span class="Apple-style-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-top: 8px; padding-right: 10px; padding-bottom: 8px; padding-left: 10px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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-top: 8px; padding-right: 10px; padding-bottom: 8px; padding-left: 10px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I want to change this gromacs top files( all the output files by amb2gmx.pl 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-top: 8px; padding-right: 10px; padding-bottom: 8px; padding-left: 10px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------------------------</pre></span><pre><span class="Apple-style-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 class="Apple-style-span" style="line-height: 25px;">------------------------------------------------------------------------------------------------</span></pre><pre><span class="Apple-style-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 class="Apple-style-span" style="line-height: 25px;">----------------------------------------------------------------------------------------------------------</span></pre><pre><span class="Apple-style-span" style="line-height: 25px; "> </span><span class="Apple-style-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 class="Apple-style-span" style="line-height: 25px; "></span><span class="Apple-style-span" style="line-height: 25px; "> amb2gmx.pl converted? Thank you very much.</span></pre><span class="Apple-style-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-top: 8px; padding-right: 10px; padding-bottom: 8px; padding-left: 10px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">My email address£ºgromacs564@126.com</pre><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial, verdana, sans-serif; font-size: 14px; line-height: 25px; padding-top: 8px; padding-right: 10px; padding-bottom: 8px; padding-left: 10px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">xiaodu</pre></span><pre>
<span class="Apple-style-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-top: 8px; padding-right: 10px; padding-bottom: 8px; padding-left: 10px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></pre></span></pre><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>