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<form enctype="multipart/form-data" method="post" action="submit.php">
  <label>Molecule in <span style="color:#FF0000"><b>mol2</b></span> format with <span style="color:#FF0000"><b>ALL</b></span> hydrogens and <span style="color:#FF0000"><b>3D</b></span> coordinates (see <a href="/SwissParam_mol2_file.html">here</a> in
    case of problem): </label><br>
  <input type="hidden" name="MAX_FILE_SIZE" value="30000000">
  <input type="file" name="mol2Files" size="50"><br><br> Please, note that for consistency with CHARMM, atoms with identical names will be renamed.<br><br>
  <div id="sib_action">
    <input type="submit"><br><br>
    <!-- <span style="color: red; font-size: 30px;"><b>SwissParam is currently under maintenance.<br> We do our best to limit the duration of this period.</b></span> -->
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</form>

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SwissDrugDesign

SwissDock
SwissParam
SwissSidechain
SwissBioisostere
SwissTargetPrediction
SwissADME
SwissSimilarity

About us
Swiss Institute of Bioinformatics


SWISSPARAM




Please, take our survey to find out how you use our tools and how we could
improve them. It only takes 8 min.


THIS SERVICE PROVIDES TOPOLOGY AND PARAMETERS FOR SMALL ORGANIC MOLECULES
COMPATIBLE WITH THE CHARMM ALL ATOMS FORCE FIELD, FOR USE WITH CHARMM AND
GROMACS.

Created and maintained by the Molecular modeling group, SIB.

The data are derived from the Merck Molecular ForceField (MMFF). Dihedral angle
terms are taken as is, while only the harmonic part of the bond, angle and
improper terms are retained. Charges are taken from MMFF. Van der Waals
parameters are taken from the closest atom type in CHARMM22.
These parameters are intended for "drug design" type calculations, like docking,
minimizations, rapid binding energy estimation (LIECE), etc... Deeper
parameterizations are required for applications in which a very fine description
of the molecule is required, (e.g. normal mode calculations...). SwissParam
results can then be used as a starting point for such a procedure.

SwissParam is automatically used by SwissDock, a web server for docking small
molecules to proteins.

This server is free for academic use. A CHARMm license is required for users
from private companies.

If you are using SwissParam, please, cite:
V. Zoete, M. A. Cuendet, A. Grosdidier, O. Michielin, SwissParam, a Fast Force
Field Generation Tool For Small Organic Molecules, J. Comput. Chem, 2011,
32(11), 2359-68. PMID: 21541964, DOI: 10.1002/jcc.21816.



Molecule in mol2 format with ALL hydrogens and 3D coordinates (see here in case
of problem):


Please, note that for consistency with CHARMM, atoms with identical names will
be renamed.









USEFUL LINKS:

 * How to obtain a correct mol2 file for use with SwissParam.
   
   
 * How to use SwissParam to setup a molecular dynamics simulation of a protein
   with a small-molecule ligand in GROMACS using the CHARMM forcefield.

Swiss Institute of Bioinformatics - 2022