On Wed, Mar 18, 2015 at 12:41 PM, Edwin Helbert Aponte Angarita <
helbert2a.gmail.com> 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.
>
I have no idea why it's not working for you. It works just fine for me
with Amber 12 and AmberTools 13 (fully updated):
swails.batman /usr/local/amber12/test/gb7_trx $ ../../update_amber --version
Version is reported as <version>.<patches applied>
AmberTools version 13.24
Amber version 12.21
if you're sure it's not working for you, then let us know what operating
system and compilers you are using to see if we can try to reproduce it
somewhere...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 18 2015 - 14:30:02 PDT
