The CELLmicrocosmos Cell Modeling projects started in SS2010. This forum contains topics relevant for this student courses at Bielefeld University. Here, also tutorials may be found, summaries as well as open discussion for improvements.
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bjoern
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Hints

Post by bjoern » 06.07.2010, 16:03

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
Attachments
LIPIDS_JENS.rar
The Membranes with the itp files from Jens. Four different Lipid Types.
(931.77 KiB) Downloaded 967 times
LIPIDS_BJOERN_HIC-UP+Sphingomyelin.zip
Lipids from HIC-UP which are not Gromacs compatible. Therefore a broad range of lipid types.
(880.82 KiB) Downloaded 1043 times

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bjoern
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Posts: 211
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Re: Hints

Post by bjoern » 27.07.2010, 13:32

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
VMD_query_representation.jpg (62.42 KiB) Viewed 14155 times

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