[gmx-users] system contains proteins and DNAs with ffamber99

Vigneshwar Ramakrishnan vmsrvignesh at gmail.com
Wed Jun 11 10:33:05 CEST 2008


I think the answer to both of your questions is YES!
Though, I have used ffamber03 for simulating protein+DNA. But I guess it
shouldn't matter.


On Wed, Jun 11, 2008 at 3:50 PM, Dechang Li <li.dc06 at gmail.com> wrote:

> Dear all,
>    Sometimes,the PDB file contains water molecules which only have the
> oxygen atom. Can
> Gromacs add the hydrogen atoms of the water molecules?
>    Additionly, when use Gromacs with the force field ffamber99, Can it add
> the hydrogen
> atoms of the DNA? Can I use the force field ffamber99 to simulate the
> system which contains
> proteins and DNAs?
> Best regards,
> =========================================
> Dechang Li, PhD Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> PR China
> Tel:   +86-10-62773779(O)
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
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Dept. of Chemical & Biomolecular Engg,
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