Thank you very much Florian! <br>It is what I want to know and I can successfully transform from amber format to gromacs format! <br><br>Sincerely, <br>Seungpyo Hong <br><br><div><span class="gmail_quote">On 8/22/07, <b class="gmail_sendername">
Florian Haberl</b> <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de">Florian.Haberl@chemie.uni-erlangen.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>On Tuesday, 21. August 2007 22:14, SeungPyo Hong wrote:<br>> Dear gmx-user,<br>> Until yesterday, I believe in PRODRG server.<br>> But when I inspect the result carefully, I found it does not make sense at
<br>> all!<br>> Of course, its because I did not modify the input and just thought all the<br>> process will be done automatically.<br>><br>> Anyhow, I also found that partial charge is not plausible even after I get
<br>> the plausible structure by adding some options in it.<br>> So, I tried amber's antechamber, and get .prepin file and the partial<br>> charge in it seems to be reasonable.<br>><br>> Then, I want to convert .prepin file into .itp file.
<br>> Is there a software doing that work?<br><br>take a look at <a href="http://wiki.gromacs.org/index.php/AMBER">http://wiki.gromacs.org/index.php/AMBER</a><br><br>You need to start tleap or xleap to generate top and crd files of your
<br>molecule, than use the perl skript (amb2gmx.pl) to transfer it to .gro<br>and .top file with gromacs format.<br>You also need to take the correct forcefield of AMBER.<br><br><br>><br>> Or, is gromacs has tool that generate topology parameters like antechamber
<br>> in amber?<br>><br>> Thank you for reading.<br><br><br>Greetings,<br><br>Florian<br><br>--<br>-------------------------------------------------------------------------------<br> Florian Haberl<br> Computer-Chemie-Centrum
<br> Universitaet Erlangen/ Nuernberg<br> Naegelsbachstr 25<br> D-91052 Erlangen<br> Telephone: +49(0) − 9131 − 85 26581<br> Mailto: florian.haberl AT <a href="http://chemie.uni-erlangen.de">chemie.uni-erlangen.de</a>
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<br>-Paul Dirac <br>'But he created too many objects.'<br>-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">
sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a>