Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center]

From: Erdem Yeler <erdemyeler.gmail.com>
Date: Sat, 8 Jan 2022 03:28:52 +0300

Dear Prof.
Thank you for your reply. Here are my instructions:
pt_sander.dat is my frcmod file. I prepared this file then I created *.top
and *.crd files using tleap:
--------------
tleap
source leaprc.gaff2
loadamberparams pt_sander.dat
a=loadmol2 01.mol2
saveamberparm a a.top a.crd
quit
-----------
After that I scanned sander:
sander -O -i min_0.in -o out_benz_furan/a_0.out -p a.top -c a.crd -r
out_benz_furan/a_0.crd &
sander -O -i min_10.in -o out_benz_furan/a_10.out -p a.top -c a.crd -r
out_benz_furan/a_10.crd &
sander -O -i min_20.in -o out_benz_furan/a_20.out -p a.top -c a.crd -r
out_benz_furan/a_20.crd &
exc...

here is my one of min_xx.in file:
------------------
 dihedral scan
 &cntrl
  imin=1,
  ntb=0,
  cut=15,
  maxcyc=1000,
  ntpr=1,
  nmropt=1
 /
 &wt type='END'
 /
 DISANG=dih_tmp/dihedral_5.f
-------------
other min files are the similar:

for 10 degree DISANG = dih_tmp/dihedral_10.f
for 15 degree DISANG= = dih_tmp/dihedral_10.f
exc...
----------
and here is my dihedral_5.f:

   &rst iat=2,1,18,27,
 r1=4.900000, r2=5.000000, r3=5.000000, r4=5.100000, rk2=5000.0,
rk3=5000.0, /

----
 dihedral_10.f:
   &rst iat=2,1,18,27,
 r1=9.900000, r2=10.000000, r3=10.000000, r4=10.100000, rk2=5000.0,
rk3=5000.0, /
---
dihedral_15.f:
   &rst iat=2,1,18,27,
 r1=14.900000, r2=15.000000, r3=15.000000, r4=15.100000, rk2=5000.0,
rk3=5000.0, /
---
exc...
*It would help a lot to know details here: which dihedrals worked, and
whichwere problematic?*
os-Pt-os-c3 is OK but
os-Pt-n4-ca, os-Pt-ca-ca ,os-Pt-n4-hn  are problematic...
Thank you..
David A Case <david.case.rutgers.edu>, 3 Oca 2022 Pzt, 18:28 tarihinde şunu
yazdı:
> On Sun, Jan 02, 2022, Erdem Yeler wrote:
>
> >I am trying to parameterize a molecule containing transition metal. During
> >scanning, the sander could not rotate dihedral in the range of 80-160
> >degrees and produced the same energy (See the chart below).
>
> It would help if you provided the exact instructions you gave to sander.
> The plot shows similar (not "the same") energy for angles in the 80-160
> degree range.  Do you know that this is wrong?
>
> >It hardly turned some dihedrals at all.
>
> It would help a lot to know details here: which dihedrals worked, and which
> were problematic?  Depending on the coordination number about the metal, it
> can be quite tricky to scan about metal-based dihedral angles.  But one
> would need to more more information than just "it didn't work" to provide
> useful suggestions.
>
> ....dac
>
>
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Received on Fri Jan 07 2022 - 16:30:02 PST