Hi,
while your leap file seems not to contain any obvious (at least to me)
problems, it's not clear what exactly you mean by "the complex got
broken", since you did neither tell us what made you think your complex
got broken and how it should look according to your setup, nor provide
us with any information about your system (protein-ligand system
covalently or non-covalently bound?).
When visualizing your system, please keep in mind that the drawing of
bonds may depend on an inner logic of the visulization software, e.g.
when you use a pdb file with just the atom positions as input programs
use a distance cutoff criterion to decide about showing a bond there or not.
Regards,
Anselm
On 06/23/2021 06:00 AM, richa anand 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 - 06:00:02 PDT
