Sorry for the autocorrect. When you loaded the mdcrd file into that
molecule what did it say?
On Mar 1, 2018 7:02 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> Then when you loaded the necessary file next, what exactly did VMD say?
>
> On Mar 1, 2018 6:44 PM, "Gu, Wenze" <wenze_gu.brown.edu> wrote:
>
>> Hi Carlos,
>>
>> Yes, I first loaded the prmtop file and then loaded the mdcrd file. After
>> loaded the prmtop file, vmd said there are 38800 atoms.
>>
>> Best,
>> Wenze Gu
>> Department of Chemistry
>> Brown University
>>
>> On Thu, Mar 1, 2018 at 2:37 PM, Carlos Simmerling <
>> carlos.simmerling.gmail.com> wrote:
>>
>> > this was just discussed a few days ago on the list, most likely you are
>> not
>> > using the right format for the file in VMD.
>> > Amber coordinates format is the trajectory file (mdcrd), restart format
>> is
>> > the restart file. did you load your prmtop first, then the mdcrd file as
>> > coordinates format (or coordinates with box)?
>> >
>> > On Thu, Mar 1, 2018 at 2:16 PM, Gu, Wenze <wenze_gu.brown.edu> wrote:
>> >
>> > > Dear list,
>> > >
>> > > I ran amber MD with this .in file:
>> > >
>> > > md, npt, equilibrium to 300K quickly,
>> > > &cntrl
>> > > imin = 0, ntx = 7, irest = 1, ig=-1
>> > > ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0, ntwr=50000,
>> > > ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
>> > > nstlim = 10000000, dt =0.002,
>> > > temp1=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
>> > > ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
>> > > &end
>> > > END
>> > > END
>> > >
>> > > However, when I tried to read the trajectory file in VMD, it says
>> > incorrect
>> > > number of atoms <0> in mdcrd file. Meanwhile, the prmtop file has
>> normal
>> > > number of atoms. Do you know what's going wrong here? Thanks!
>> > >
>> > > Best,
>> > > Wenze Gu
>> > > Department of Chemistry
>> > > Brown University
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Received on Thu Mar 01 2018 - 16:30:02 PST
