6.17 Save the molecule

VEGA ZZ uses customized file requesters, allowing to select some options:


Save dialog


To show this dialog box, you must select File Save main menu item or click the disk picture of the Tool bar 1. You can choose the File name and the file format (Save as), but you can also select the Compression mode (None, BZip2, GZip and Z Compress) and the possibility to save the Connectivity and the atom Constraints for the molecular dynamics. Two file formats only are able to store constraint data and they are PDB (in the B column for NAMD) and IFF/RIFF. The Big endian and 64 bit checkboxes are specific for IFF/RIFF format. The former allows to write in big endian format (it's the real IFF written by old VEGA releases) and the latter switches the saver in 64 bit mode in order to write files larger than 4 Gb.
Selecting AMMP and X-Plor PSF  file formats, it's possible to enable the force field parameter check (Force field parm. combo box), in order to fix the missing parameters if they aren't included in the parameter files. If one or more parameters aren't included, the missing parameter table is shown.
The supported file formats are: PDB 2.2 (*.pdb), PDB (*.pdb), PDB non std (*.pdb), PDB Atdl (*.pdb;*.pdba), PDB Fat (*.pdb;*.pdbf), PDBQ (*.pdb), PQR, (*.pqr), PQR XML (*.xml), Insight (*.car), Old Insight (*.car), Alchemy (*.alc;*.mol), AMMP (*.amp), AutoDock 4 PDBQT (*.pdbqt), AutoDock Vina PDBQT (*.pdbqt), ChemSol (*.cs), CIF (*.cif), mmCIF (*.cif), CML 2.0 (*.cml), CML (*.cml), CPMD XYZ (*.xyz), CRD (*.crd), CRT (*.crt), Cssr (*.cssr;*.csr), Fasta (*.fas), Gamess (*.inp), Gaussian cartesian (*.gjf), Gromacs/Gromos (*.gro), Gromacs/Gromos nm (*.gro), IFF/RIFF (*.iff), InChI (*.inchi; *.inc), InChI + Aux (*.inchi; *.inc), InChIKey (*.ikey), Indigo layered code (*.indigo), Info XML (*.xml),  MDL Mol (*.mol), Mol2 (*.ml2;*.mol;*.mol2), Mopac (*.dat;*.arc), Mopac cartesian (*.dat;*.arc), Quanta MSF (*.msf), QMC (*.qmc), SMILES (*.smi), X-Plor PSF (*.psf), XYZ (*.xyz).


IFF files are compatible with old VEGA releases (pre-2.0.6 and pre-1.5.6) saving them in 32 bit big endian format (Big endian checked and 64 bit unchecked).