[ghemical-users] question about the gpr format

[Tommi Hassinen]

Hello,

I'm trying to answer quickly now, even though I don't have any .gpr file
or the source code available right now.

But in the .gpr file format, you should in !Atoms section define the atoms
with their atomic numbers (value 6 = carbon in the example below), their
formal charges (value +0 below) and some extra information (4096 below
but you should set it to 0 initially). I cannot tell (=don't remember) what
4096 is for. About the atom names, there is no such record in .gpr format
yet.

Further, the bonding information is defined in a !Bonds section and 
the atom x,y,z coordinates are defined in !Coord section of a .gpr
file.

I hope this helps,
Tommi H.

________________________________________
From: ghemical-users-bounces at bioinformatics.org [ghemical-users-bounces at bioinformatics.org] On Behalf Of silvia.imberti at stfc.ac.uk [silvia.imberti at stfc.ac.uk]
Sent: Friday, November 05, 2010 5:04 PM
To: ghemical-users at bioinformatics.org
Subject: [ghemical-users] question about the gpr format

Dear Ghemical experts,

I have two questions about the gpr format.

1)      I have two ways of producing a .gpr, one way is directly from Ghemical, and I obtain this:

!Header gpr 100

!Info 1

!Atoms 39

0 6 +0 4096

1 6 +0 4096

2 6 +0 4096

3 6 +0 4096

4 6 +0 4096

5 6 +0 4096

6 6 +0 4096

………..

The other way is my converting a .pdb file into a .gpr and I obtain this:

!Header gpr 100

!Info 1

!Atoms 39

0 6

1 6

2 6

3 6

4 6

5 6

6 6

7 6

8 6

…………

As you can see in the first way I obtain some extra characters “+0 4096”. Can someone explain to me what they represent, what’s their role?

2)      The second question is about atom names. Is there a way to carry on atoms labels from the pdb, or to input them into the gpr format?

C1, C2, C3, and then H1 and O1 connected to C1, HO1 connected to O1…..

Thanks in advance, Silvia

Silvia Imberti

Instrument Scientist

ISIS neutron and muon source

Rutherford Appleton Laboratory


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