VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 18 2013 - 09:48:34 CDT

On Wed, Sep 18, 2013 at 3:32 PM, Yunjie Zhao <yjzhao.wh_at_gmail.com> wrote:
> Hi,
>
> Thanks for the quick reply. How to provide the suitable topology file
> matched with the force field? The pdb file does not have any hydrogens when

what *is* your force field? standard pdb files from the PDB almost
never have hydrogens (since they are near invisible for x-ray).
have a look at the psfgen and NAMD tutorials and see how things work.

> I am doing the Automatic PSF Builder. I want to generate the psf file with
> the atoms exactly as the input pdb file. Could you please tell me how to do
> this with more details? Thanks a lot.

if you want more details, you have to *first* _provide_ more details.
what do you need the PSF file for? where are the parameters going to
come from?

unless you can provide a reasonable explanation why there should not
be any hydrogens, even though you select a force field that contains
them, it will be impossible to give an answer that will satisfy you,
since with the current information, what you are asking for makes no
sense.

axel.

>
> Regards,
> Yunjie
>
>
> On Wed, Sep 18, 2013 at 9:30 AM, Yunjie Zhao <yjzhao.wh_at_gmail.com> wrote:
>>
>> Hi,
>>
>> Thanks for the quick reply. How to provide the suitable topology file
>> matched with the force field? The pdb file does not have any hydrogens when
>> I am doing the Automatic PSF Builder. I want to generate the psf file with
>> the atoms exactly as the input pdb file. Could you please tell me how to do
>> this with more details? Thanks a lot.
>>
>> Regards,
>> Yunjie
>>

> --
> Yunjie Zhao, PhD
> Department of Physics
> The George Washington University 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.