CELLmicrocosmos.org forum

[bjoern]

PDB Format Documentation

All about the PDB Format:
http://www.wwpdb.org/docs.html

The actual format directly as HTML:
http://www.wwpdb.org/documentation/format32/v3.2.html

[bjoern]

VMD Hints

How to throw out all water and ions inside a specified radius of the intra-membrane atoms using VMD Selections (based on Gunthers approach):

Goto Graphical Representations, choose Selections tab and type in 'Selected Atoms':

not ((resname 'W' 'NA+') and within 5.5 of (not resname 'W' 'NA+'))

Then goto File -> Save coordinates, choose pdb as File type, and as Selected Atoms the term described above and Save.

A better query is:

not ((resname 'SOL' 'NA+') and same residue as within 5.5 of (not resname 'SOL' 'NA+'))

Here, 'SOL' is e.g. for ffG45a3. 'W' is usually used for MARTINI water.

'same residue' prevents that single water molecules are broken up during export!

An alternative is

not (resname SOL and same residue as (z>20 and z<83))

Here, just all molecules water molecules within a predefined range are deleted. Of course, the values of 20 and 83 have to be adjusted to your membrane.

VMD_query_representation.jpg (62.42 KiB) Viewed 18746 times