<div style="font-family: 'Times New Roman'; font-size: 16px;"><br />Check the topology section in the gromacs manual. <br _moz_dirty="" />You'll find the format you should use for bonds, angles etc.<br _moz_dirty="" /><br /><span>On 15-02-11, <b class="name">gromacs564 </b> <gromacs564@126.com> wrote:</span><blockquote cite="mid:6082467e.573d.12e2889e79a.Coremail.gromacs564@126.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div style="color: rgb(0, 0, 0); font-size: 14px; font-family: arial,verdana,sans-serif; line-height: 1.7; padding: 8px 10px; margin: 0px; background-color: rgb(255, 255, 255);">Dear All:<div><div> I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter.</div><div> I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate:</div><div><br /></div><div>-------------------------------------------------------<br />Program grompp_m, VERSION 4.5.1<br />Source code file: toppush.c, line: 1631<br /><br />Fatal <span class="t_tag" href="tag.php?name=error">error</span>:<br />Incorrect number of parameters - found 1, expected 2 or 4 for Bond.<br />For more information and tips for troubleshooting, please check the GROM···<br />--------------------------------------------------------------------------------------------<br /></div><div ><br/></div><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif;"><br /></pre><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif;">I added some bonds and angles <span class="Apple-style-span" style="white-space: normal;">parameters like this:</span></pre><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif;"><span class="Apple-style-span" style="white-space: normal;">······························<br />; residue 44 ASN rtp ASN q 0.0<br /> 664 N 44 ASN N 664 -0.430106 14.01 ; qtot 4.57<br /> <font color="red">665 HD 44 ASN HD 665 0.250466 2.016</font> ; qtot 4.824<br /> 666 CT 44 ASN CA 666 0.044609 12.01 ; qtot 4.869<br />···············<br />[ bonds ]<br />; ai aj funct c0 c1 c2 c3<br />···<br /> 676 678 1 <br /> 678 679 1 0.10115 <br /> 678 680 1 <br /> 680 681 1 <br />·······················<br />[ angles ]<br />; ai aj ak funct c0 c1 c2 c3<br />························<br /> 648 650 652 1 <br /> 651 650 652 1 115.149 <br /> 650 652 653 1 <br /> 650 652 654 1 <br />····················<br /></span></pre><pre style="white-space: pre-wrap; word-wrap: break-word; font-family: arial,verdana,sans-serif;"><span class="Apple-style-span" style="white-space: normal;">Any help will highly appreciated!</span></pre></div></div><div><div ><br/></div><pre></pre></div><br /><br /><span title="neteasefooter"><span id="netease_mail_footer"></span></span></div></blockquote></div>