Hi,<br><br>genbox can now modify the topology file by using genbox ... -p topol.top. <br><br>Best,<br><br>Matthias Schmidt<br><br>On Friday, August 5, 2011, lina <<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>> wrote:<br>
> On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman<br>> <<a href="mailto:ravikumarvenkatraman@gmail.com">ravikumarvenkatraman@gmail.com</a>> wrote:<br>>> Dear all,<br>>> I have generated .gro and .top file for Chloranil from prodrg<br>
>> and tried solvate it using p<br>re-equilibrated cyclohexane. When i tried to<br>>> generate the box containing solute it is not modifying the .top file and it<br>>> shows zero solvent.<br>>> Please help me how to solvate organic molecules that are obtainde from<br>
>> prodrg.<br>>><br>>> Thank you.<br>><br>><br>> Try:<br>><br>> genbox -cp chloranil.gro -cs cyclohexane.gro -o system.gro<br>><br>><br>> and manually modify the topol.top later.<br>
><br>> you may use the solvated pre-equilibrated cyclohexane as<br>> cyclohexane.gro, so no need add water later.<br>><br>> It should be no problem.<br>>><br>>> --<br>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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>><br>><br>><br>><br>> --<br>> Best Regards,<br>><br>> lina<br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>
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><br><br>-- <br>Best,<br><br>Matthias<br>-- <br>Structural Bioinformatics and Computational Biochemistry Unit<br>Dept. of Biochemistry<br>University of Oxford<br> <br><a href="http://sbcb.bioch.ox.ac.uk/schmidt.php" target="_blank">http://sbcb.bioch.ox.ac.uk/schmidt.php</a><br>
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