Dear All,
I am sorry I forgot to mention that I am using Amber v12.0.
Regards,
Edwin.
On Wed, 2015-03-18 at 16:41 +0000, Edwin Helbert Aponte Angarita wrote:
> Dear All,
>
>
> I am able to write the trajectory of a minimization of a peptide
> salvated in TIP3PBOX. I have used this .in file
>
> &cntrl
> imin=1,
> maxcyc=20000,
> ncyc=4000,
> cut=10.0,
> ntb=1,
> ntr=0,
> ntpr=100,
> ntwx=100,
> ioutfm=1,
> /
>
>
>
> Then I calculate the rmsd to the first frame using ptraj and whith:
> trajin ./min.mdcrd
> rms first out rmsd_to_first.dat .N,CA,C
>
>
> and I get a very nice plot showing how the peptide converges to a
> local minimum and does not change noticeable any more. However, I
> cannot get sander nor sander.MPI to write the trajectory file if I use
> generalized Born implicit solvent. In that case I use:
>
> &cntrl
> imin=1,
> maxcyc=2000,
> ncyc=1000,
> cut=999.,
> rgbmax=999.,
> igb=1,
> ntb=0,
> ntpr=50,
> ntwx=50,
> ioutfm=1,
> /
>
>
> and I am setting approppriatelly -i -o -p -c -r -x.
>
>
> Do you know how can I get the trajectory when using generalized Born
> implicit solvent? I only found a very old similar post
> (http://archive.ambermd.org/200502/0076.html) but is not really
> helpful.
>
>
>
> Thanks,
>
>
> Edwin.
>
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Received on Wed Mar 18 2015 - 13:30:06 PDT
