= Frequently Asked Questions =

Here you can find answers to some of the most frequently asked questions about using MoleCuilder's various interfaces. If you have a question not answered on this page, you can ask it on the MailingList or via email.

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== Command Line == #command-line

=== Output Files === #command-line_output-files

==== I need the output in format <specific-format> ====

Remember that molecuilder always operates on an output file given by the ''--input'' command. It does recognize the format (by the suffix) if the file is empty (e.g. newly created). Also, additional output formats may be specified. This is done by ''--set-output'' followed by a space-separated list of desired formats, e.g.
{{{
 ... --set-output tremolo pcp xyz
}}}

==== I am using tremolo, but it does not recognize '''HT''' (specific element types) ====

Molecuilder always operates on elements, i.e. for each atom it needs to know what kind of element it consists of. With empirial potential molecular dynamics, such as represented by tremolo, element short hands are replaced by a type symbol to allow for different paramtrization of hydrogen in water and hydrogen in some other molecule: e.g. '''HT''' may stand for hydrogen in water, where '''H1''' describes a hydrogen in a specific ligand of a bio molecule.

Molecuilder does not initially know what '''HT''' or '''H1''' means (although it does some guessing in the case of pdb format). Hence, you have to tell him what is what. Tremolo uses a ''.potentials'' file to give the element for a given type key. This can be parsed as follows (before the ''--input'' command!):
{{{
  .. --parse-tremolo-potentials <.potentials file>
}}}