Actually, I only input a pdb file to get the normal modes, and then the
used force field is leaprc.ff14SB, so I don't know if this is really an
option
On Tue, Nov 22, 2016 at 9:30 AM, The Cromicus Productions <
thecromicusproductions.gmail.com> wrote:
> I'll try that and let you know!
>
> On Tue, Nov 22, 2016 at 8:11 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Mon, Nov 21, 2016, The Cromicus Productions wrote:
>> >
>> > I'm currently working with NMA in nab. I can simulate the modes
>> > and get the frequencies with the code below. I'm working with DNA.
>> > Say I want to pin both extremes (residues 1,10,11 and 20 for example)
>> > for my NMA to see "perfect wave" motions, is this possible? What should
>> > I modify to the code?
>>
>> One idea: modify your prmtop file to make the masses of the end residues
>> very
>> large. The recompute the normal modes. The atoms at the end will not
>> move
>> very much.
>>
>> ....dac
>>
>>
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Received on Tue Nov 22 2016 - 07:00:05 PST
