PDB file generator

[apricimo]

Looking for a way to create a molecule and then spit out molecular coordinates in pdb format

 

help please

 

I should mention I am using a mac

 

open source software is welcomed

Edited February 16, 2011 by apricimo

[CaptainPanic]

What are "molecular coordinates"? Do you mean the bond angles and bond lengths?

 

The only program that I know that comes close to what you want to do is chemdraw, but that's a Windows program... and probably not exactly what you're looking for.

Why do you use an apple machine for such scientific tasks? I know only people who use Windows or Linux for scientific work. And even for those systems, the program you want might not exist.

[hypervalent_iodine]

What are "molecular coordinates"? Do you mean the bond angles and bond lengths?

 

The only program that I know that comes close to what you want to do is chemdraw, but that's a Windows program... and probably not exactly what you're looking for.

Why do you use an apple machine for such scientific tasks? I know only people who use Windows or Linux for scientific work. And even for those systems, the program you want might not exist.

 

Not true. I have ChemDraw on my mac and it works just fine

 

Re. the OP. Are you looking for something that can model small compounds or protein type structures?

[apricimo]

What are "molecular coordinates"? Do you mean the bond angles and bond lengths?

 

The only program that I know that comes close to what you want to do is chemdraw, but that's a Windows program... and probably not exactly what you're looking for.

Why do you use an apple machine for such scientific tasks? I know only people who use Windows or Linux for scientific work. And even for those systems, the program you want might not exist.

 

Why not?

 

Anyway since posting this I figured out how to do all of it on a mac. So now you can't say that people ONLY use Windows and Linux for scientific work. Unix is a popular computing platform and that's what a mac is a UNIX.

[timo]

Might still be cool if you posted what you actually were asking for (it didn't really become clear to me) and, in case someone with a similar question reads this thread at some point in the future, what your solution is.

 

@Captain Panic: I think all scientific programs I've been using come as source code and seem to compile on Linux as well as on Mac (checked for gromacs, ROOT, Sherpa, Pythia, the BOOST libraries, and the killer application: gnuplot).

[apricimo]

Might still be cool if you posted what you actually were asking for (it didn't really become clear to me) and, in case someone with a similar question reads this thread at some point in the future, what your solution is.

 

@Captain Panic: I think all scientific programs I've been using come as source code and seem to compile on Linux as well as on Mac (checked for gromacs, ROOT, Sherpa, Pythia, the BOOST libraries, and the killer application: gnuplot).

 

So for example if I take a pdb of some protein from RCSB and I want to design a drug for it. HIV protease inhibitor, for example, in my case I am using AutodockTools with VINA so I need to have a pdb of the protein and the molecule I am docking also in pdb format.

 

 

Hope that is clear

 

I ended up using VMware fusion with Windows XP and ran Spartan with ChemDraw to draw my molecule and generate pdb style coordinates but it can be done also on a website called http://davapc1.bioch.dundee.ac.uk/prodrg/

[timo]

It's kind of clear. I didn't expect that you can define the topology (the connections between the atoms) and get a reasonable and reliable geometry (connections plus spatial arrangement) out of it, which is why I was skeptical of your question.

[apricimo]

It's kind of clear. I didn't expect that you can define the topology (the connections between the atoms) and get a reasonable and reliable geometry (connections plus spatial arrangement) out of it, which is why I was skeptical of your question.

 

define topology with Spartan or with the server website?

 

The energy minimisation in Spartan is on par with any other QM program out there (Gaussian).

Edited March 2, 2011 by apricimo