PDB file for Gaussian

[MingyuSun]

I hope to get a PDB file for Gaussian, I get one here http://w3dna.rutgers.edu/rebuild/ at first stage, but I cannot open it with GaussView 5.0. What I should do? And I have to make some change in the original DNA, how can I make it? The original one I got is in the attachment.

[xiangjun]

I do not use Gaussian, or GaussView for that matter. However, the attached PDB structure can be visualized with Jmol and PyMOL without a problem. For Gaussian calculations, you may well need to perform some preparations from a 3DNA-generated PDB file (adding hydrogen atoms etc), as is the case for molecular dynamics (MD) simulations. A similar procedure should also be necessary for a B-DNA structure downloaded from the PDB (e.g., 355d). Please consult Gaussian docs or local experts on those technical issues.

HTH,

Xiang-Jun

[MingyuSun]

I am really grateful for your reply! To be honest, I proceed slowly, but I really benefit from your forum and have fun doing this. Thank you very much!
You mentioned that I need to add hydrogen atoms etc, do you know how to make it? Is there any suitable software or could you suggest some reading materials?

Yours
Mingyu

[xiangjun]

Since you mentioned Guassian, your best bet is look into materials for that QM package. Start from the simplest possible case. How Guassian has be used to perform calculations from a PDB file? There must be some tutorials on such topics. As mentioned previously, however, I am not an expert in this field.

Xiang-Jun

[MingyuSun]

Thanks a lot! I will.
I just tried some PDB file in x3dnav2.3\examples\analyze_rebuild, some can work with Gaussian, (some other PDB file in x3dnav2.3 can as well). I don't know why. But could I use this materials, I mean x3dnav2.3, to make change for my original one directily?

[xiangjun]

Since you have installed 3DNA v2.3 successfully, you can easily generate any regular B-DNA (or A-DNA) models with the fiber command. Simply type fiber -h and fiber -m for more info. The w3DNA interface calls the fiber command of 3DNA v2.0 to accompany the 2008 Nature Protoctols.

From the info you provided, I sense that the issue you experienced could be due to PDB format change. For example, in the w3DNA-generated PDB file (with 3DNA v2.0), the two non-bridging phosphate oxygens are labeled O1P/O2P which have been renamed OP1/OP2 following the current PDB v3 format.

Glad yo see you've made some progress. You may want to stay with 3DNA v2.3 instead of using w3DNA for your PDB models.

Xiang-Jun

[MingyuSun]

I am really sorry keep bothering you. But in fact, I have not successfully install that. I tried to run it with cmd, but failed. I tried to install MinGW Ruby, I should have installed them.When I click MinGW, I got a screen, but I still cannot install 3DNA v2.3. I put two screenshots in the attachments explaining my situation. I do not know why I can't paste them here directily.
As for the MinGW, there are two potential problems. I did not see "blur" as mentioned on the website. And there is only one "fstab.sample" that cannot be opened in the place that "fstab" should be, I created a txt name "fstab" and only wrote C:\MinGW   /mingw there.
Do you know how to fix that?

[xiangjun]

I am glad you brought up this installation issue again. Please follow what I've requested in the original thread. Your first screenshot shows that you are still using Windows cmd instead of MinGW/MSYS. If Linux is not an option for your, Cygwin is a better choice than MinGW/MSYS to avoid confusion from Windows cmd. Please show us a screenshot of your successful installation of Cygwin.

You are trying to achieve too many things at the same time. Let's focus on installing DSSR first, then 3DNA v2.3, and then PDB files in Gausian. Please follow instructions step-by-step, and put each separate topic in a new thread. This current thread is already a mix-up of 2+ topics.

3DNA-related questions are always welcome on the Forum. So you should not feel sorry for 'bothering' me. I just hope you could follow my request one at a time, and summarize what've learned along the way. Your experience may well help other new 3DNA users, and that's the point of the Forum.

One more point: 3DNA (especially the new DSSR program) has been designed to be easy to install. It should take no more a few minutes to get software up and running. Asking a local expert for help over the initial setup process would be very beneficial in a situation like yours.


Xiang-Jun