VMD-L Mailing List

From: Yunjie Zhao (yjzhao.wh_at_gmail.com)
Date: Wed Sep 18 2013 - 08:32:07 CDT

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

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
>
>
> On Wed, Sep 18, 2013 at 4:22 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>> On Wed, Sep 18, 2013 at 8:57 AM, Yunjie Zhao <yjzhao.wh_at_gmail.com> wrote:
>> > Hi,
>> >
>> > I have generate a psf file from the pdb structure using Automatic PSF
>> > Builder in VMD. However, it adds the hydrogen atoms as well. I want to
>> > remove all the hydrogen atoms from the generated psf file.
>>
>> yes, it will generate a psf file according to the topology file that
>> you provide. that is how this works. if you want to have autopsf to
>> not generate these, you need to supply a suitable topology file. this
>> has to match your force field as well. if you simply strip off the
>> hydrogens, you will have thoroughly inconsistent parameters assigned
>> to your atoms.
>>
>> axel.
>>
>>
>>
>> > I am trying to use psfgen.
>> > resetpsf
>> > readpsf myfile.psf
>> > coordpdb myfile.pdb
>> > mol load psf myfile.psf pdb myfile.pdb
>> > set bad [atomselect top "hydrogen"]
>> > foreach segid [$bad get segid] resid [$bad get resid] name [$bad get
>> name]
>> > {delatom $segid $resid $name}
>> >
>> > But, this does not work.
>> >
>> > What's wrong with this? Thanks for any help and explanation.
>> >
>> > Regards,
>> > Yunjie
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>
>
> --
> Yunjie Zhao, PhD
> Department of Physics
> The George Washington University
> 

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