Hi,
Sounds like it could be a visualization artifact. To see if it is, try
running the minimization with coordinate wrapping off (i.e. 'iwrap=0')
or use cpptraj to reimage the coordinates/restart (via e.g. the
'autoimage' command).
Hope this helps,
-Dan
On Wed, Jun 23, 2021 at 12:00 AM richa anand <richaaanand.gmail.com> wrote:
>
> Dear Users,
>
> I am trying to simulate "protein-ligand complex", for which the Tleap input
> parameters used are given below:
>
>
> source leaprc.protein.ff14SB
>
> source leaprc.gaff
>
> source leaprc.water.tip3p
>
> loadamberprep UNK_clean_H.prepi
>
> loadamberparams UNK.frcmod
>
> COMPLEX = loadpdb complex_clean_H.pdb
>
> check COMPLEX
>
> addions COMPLEX Cl- 1
>
> solvateOct COMPLEX TIP3PBOX 12.00
>
> charge COMPLEX
>
> saveAmberParm COMPLEX complex.prm.top complex.prm.crd
>
> savepdb COMPLEX complex_out.pdb
>
> quit
>
>
> but when I extracted the pdb file after minimization of 1000 steps, the
> complex got broken. While, the energy seems ok. All parameters in energy
> file is ok. Is this (breaking of molecule) the problem of improper force
> field or water model.
> For once I had faced the same problem with protein-RNA complex, but that
> time I changed solvatBox to solvateOct and it worked. BUt, unfortunately
> it's not working this time.
> KIndly suggest me what to do?
>
>
>
>
> Thanking You,
> Richa
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 23 2021 - 06:30:03 PDT
