From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Tue May 23 2006 - 14:47:00 CDT

An update to item 3 in my previous message (previous message repeated at the end of this email).

 OK, I just found out that, when I load my psf and my pdb files into VMD, it refuses to read all the bonds.

I get the following output:

 

"...

ERROR) MolAtom 1: Exceeded maximum number of bonds (8).

ERROR) MolAtom 3: Exceeded maximum number of bonds (8).

ERROR) MolAtom 5: Exceeded maximum number of bonds (8).

ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom coordina

tes are in the wrong units?

ERROR) BaseMolecule: Silencing bonding error messages.

Info) Analyzing structure ...

Info) Atoms: 32

Info) Bonds: 60

Info) Residues: 9

Info) Waters: 0

ERROR) Residue 3 exceeded maximum number of bonds (4).

Info) Segments: 1

Info) Fragments: 2 Protein: 0 Nucleic: 0

Info) Using plugin pdb for coordinates from file /home6/acv12/AuAC_2_2_2_new.pdb

Info) Finished with coordinate file /home6/acv12/AuAC_2_2_2_new.pdb"

 

This means that it is able to read all the atoms (32) but it doesn't read all the bonds. It only reads 60, not the total number of bonds I have.

Since I am simulating gold in a cubic close packed structure, each gold atom has 12 first neighbors, which I list as 12 bonds (exception made to the atoms at the surfaces, which have 8 neighbors). Is this a problem for VMD?

 

Thanks,

 

Ana

_________________________________

Ana CÚlia Ara˙jo Vila Verde

Penn State University

Department of Chemical Engineering

Fenske Laboratory
University Park, PA 16802

USA

 

Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

avilaverde_at_engr.psu.edu

_________________________________

-----Original Message-----
From: Ana Celia Araujo Vila Verde
Sent: Tuesday, May 23, 2006 12:37 PM
To: 'vmd-l_at_ks.uiuc.edu'
Subject: the crystal structure of gold: questions about making the psf and about visualization in VMD

 

Hi,

 

I made a pdb and a psf file for gold, to be used in NAMD. I have three questions:

 

1 - when I make the bond list in VMD, is it a problem if I repeat bonds? For example, let's say that atom 1 is connected to atom 2. In the bond list, should I list this bond just once ( "1 2") or can I list it twice ("1 2 2 1")? Also, if I only list it once, does it matter if I use "1 2" or "2 1"? I couldn't find information about this.

 

2 - I will use periodic boundary conditions in my simulation. So, my crystal should also be periodic. Should I just list the realistic bonds or should I also include the bonds that make the crystal periodic? Here's a 1-dimensional example:

The realistic bonds are 1-2, 2-3, 3-4. However, to make this 1-dimensional crystal periodic, I need to connect 1 to 4. So, should the psf include bond "1-4"?

 

1-------2-------3---------4

 

3- I currently have a pdb and a psf already done. My current psf includes repeated bonds (like I described above in 1) and also includes the bonds that make the crystal periodic. When I load both the pdb and the psf file into vmd, vmd is unable to display some of the bonds correctly: some bonds do not appear at all, even though they are listed in the psf file. Also, VMD also shows the bonds between atoms in the extremities of the crystal (corresponding to the 1-4 bond described above in 2).

 

I'd really appreciate some insight into this, since I couldn't find a detailed description of the psf files that answered my questions.

Best regards,

 

Ana

 

_________________________________

Ana CÚlia Ara˙jo Vila Verde

Penn State University

Department of Chemical Engineering

Fenske Laboratory
University Park, PA 16802

USA

 

Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

avilaverde_at_engr.psu.edu

_________________________________