apricimo Posted February 16, 2011 Share Posted February 16, 2011 (edited) 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 Link to comment Share on other sites More sharing options...
CaptainPanic Posted February 18, 2011 Share Posted February 18, 2011 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. Link to comment Share on other sites More sharing options...
hypervalent_iodine Posted February 19, 2011 Share Posted February 19, 2011 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? Link to comment Share on other sites More sharing options...
apricimo Posted February 28, 2011 Author Share Posted February 28, 2011 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. Link to comment Share on other sites More sharing options...
timo Posted February 28, 2011 Share Posted February 28, 2011 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). Link to comment Share on other sites More sharing options...
apricimo Posted March 1, 2011 Author Share Posted March 1, 2011 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/ Link to comment Share on other sites More sharing options...
timo Posted March 1, 2011 Share Posted March 1, 2011 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. Link to comment Share on other sites More sharing options...
apricimo Posted March 2, 2011 Author Share Posted March 2, 2011 (edited) 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 Link to comment Share on other sites More sharing options...
Recommended Posts
Create an account or sign in to comment
You need to be a member in order to leave a comment
Create an account
Sign up for a new account in our community. It's easy!
Register a new accountSign in
Already have an account? Sign in here.
Sign In Now