Dear Amber Users,
Sorry ,I have written some wrong. It is
not cntrl namelist. It is data name list.
And, not increase, do I have to decrease drms value? Extremely sorry
for mistake.
Sanjib
On 8/29/12, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Dear Amber User,
> I want to do nmode analysis. I don't have
> access of IMSL library. So, at first I minimized my protein in sander.
> Then for nmdoe analysis I gave command like following:
> $AMBERHOME/exe/nmode -O -i nmdin -o nmdout -p protein.prmtop -c
> protein_min.rst -v vecs.
> My nmdin file is like following:
> normal mode analysis
> &cntrl
> ntrun = 1,
> maxcyc = 0,
> nvect = 12309,
> ismem = 0,
> ilevel = 6,
> ivform = 1,
> ntx = 1,
> ntxo = 0
> t = 300.00
> /
> But nmode is not running and showing a error like -
>
> Root-mean-square gradient of input coords is 2.05278199572829
> This is greater than the requested maximum: 1.000000000000000E-005
>
> Do I have to increase drms value? Actually I don't want to minimize
> the system. It is already minimized. I want to analyze nmode directly.
> So what should I do? Please help..
>
> sanjib
>
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Received on Wed Aug 29 2012 - 06:00:06 PDT
