<div>Dear gmx-users,</div>
<div> I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol simulation.But I don't even know how to start it.</div>
<div> Is it necessary to start my simulation with a .pdb files?If so,What should I do before this?I can make an pdb file for a chain of syndiotatic polyvinyl-alcohols via Material Studio or some other packages,but the residue cann't be recognize,so I have to modify some top files to correct it.I just modify the .hdb and rtp files endeavor to make it.But it seems not an easy work.</div>
<div> the message the package sent to me is as follows,appreciate if somebody can help me to handle this!</div>
<div>*** (this is an previous version.when i try to use pdb2gmx to get its .top file,a fatal error reminds:</div>
<div> "source code file : resall.c line:279 ()</div>
<div> Fatal errors:</div>
<div> in .rtp file at line : "</div>
<div> when I add the charge and chargegroupndx of the atoms,there comes a similar error ):</div>
<div>My attempt is as follows:</div>
<div>### in rtp file</div>
<div>[ VAB ]<br> [ atoms ]<br> CB opls_135<br> HB1 opls_140<br> HB2 opls_140<br> HB3 opls_140<br> CA opls_158<br> HA1 opls_140<br> OH opls_154<br> HO opls_155<br> <br> [ bonds ]<br> CB HB1<br> CB HB2<br>
CB HB3<br> CB CA <br> CA HA1<br> CA OH<br> OH HO<br> CA +CB<br> <br>[VA ]<br> [ atoms ]<br> CB opls_136<br> HB1 opls_140<br> HB2 opls_140<br> CA opls_158 <br> HA1 opls_140<br> OA opls_154<br>
HOA opls_155<br> CG opls_136<br> HG1 opls_140<br> HG2 opls_140<br> CD opls_158<br> HD opls_140<br> OD opls_154<br> HOD opls_155 <br> <br> [ bonds ]<br> CB -CA<br> CB HB1<br> CB HB2<br>
CB CA<br> CA HA1<br> CA OH<br> OH HO<br> CA CG<br> CG HG1<br> CG HG2<br> CG CD<br> CD HD<br> CD OD<br> OD HOD<br> CD +CB<br> <br>[VAE]<br> [ atoms ]<br> CB opls_136<br>
HB1 opls_140<br> HB2 opls_140<br> CA opls_157 <br> HA1 opls_140<br> HA2 opls_140<br> OH opls_154<br> HO opls_155<br> <br> [ bonds ]<br> CB -CD<br> CB HB1<br> CB HB2<br> CB CA<br> CA HA1<br>
CA HA2<br> CA OH<br> OH HO</div>
<div> </div>
<div>#### in .hdb file:</div>
<div>; H add type H i j k<br>VAB 3<br>3 4 HB CB CA +CB<br>1 5 HA CA CB +CB<br>1 2 HO OH CA +CB<br>VA 6<br>2 6 HB CB CA -CA<br>1 5 HA CA CB CG<br>1 2 HOA OA CA CG<br>2 6 HG CG CA CD<br>1 5 HD CD CG +CB<br>
1 1 HOD OD CD CG<br>VAE 3<br>2 6 HB CB CA -CD<br>2 6 HA CA CB +CB<br>1 2 HO OH CA +CB</div>