<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><span style="font-family: times new roman,new york,times,serif;">On Fri, Jul 31, 2009 at </span><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">5:19:19 PM, </font><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">Nancy <nancy5villa@gmail.com> wrote:</font><br>> If it necessary to manually create force field parameters for each
molecule, then how can one run a<br>> simulation involving a number of
arbitrary molecules (e.g. a set of mono and disaccharides) for<br>> which
there are no existing force fields?<br>
> <br>> Do you know of any other MD software package that is capable of
running simulations on<br>> arbitrary molecules without having to "piece
together" a force field for each molecule?<br><br>Provided that the desired force field has suitable parameters for a particular bonding situation<br>already, there are software packages that can generate a potentially suitable topology from<br>a molecule's structure. For gromacs topologies, user contributions to gromacs include<br>topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields<br>(my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and<br>topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions<br>is ambconv that takes the file generated by antechamber and leap from amber tools<br>and generates a gromacs topology that uses the amber or gaff forcefield selected when<br>leap was applied to the antechamber output. Another option is the Perl script<br><span>mktop at <<a target="_blank"
href="http://labmm.iq.ufrj.br/mktop/">http://labmm.iq.ufrj.br/mktop/</a>>, documented in Ribeiro, A.A.S.T., Horta, B.A.C.,</span><br>and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also<br>there is acpypi, the AnteChamber Python Parser Interface available at<br><span><<a target="_blank" href="http://code.google.com/p/acpypi/">http://code.google.com/p/acpypi/</a>>.</span><i><a id="project_summary_link" href="http://code.google.com/p/acpypi/" style="text-decoration: none;"></a></i><div style="color: black; background-color: transparent;" id="psum">
</div><br>I hope one of these with careful selection of the force field will be helpful to you.<br><br><br>Sincerely,<br><div> </div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<br><br></div><br>
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