On Wed, Jun 07, 2023, Bhattacharjee, Sinjini wrote:
>
>1. As a first step I tried only setting up the protein and non-standard
>residues (eg. Hemes, FES clusters), without the lipid bilayer.
>2. I used check in cpptraj to remove all bad contacts and based on the atom
>name printed in NSTEP1 manually.
>3. Then I do minimization with cpu version of sander in Amber20 and Still
>it gives me the following error:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 4.1424E+03 HB2 6514
>
> BOND = 7826.5578 ANGLE = 6795.2519 DIHED = 24953.4886
> VDWAALS = NaN EEL = -1339783.3680 HBOND = 0.0000
> 1-4 VDW = NaN 1-4 EEL = 80816.4521 RESTRAINT = 0.0000
>
You are describing what your intent was, not what you actually did.
1. How (exactly) did you manually remove bad contacts? How many were
removed? (As I suggested before, start just with those with zero non-bonded
distance.) Did they involve hydrogens?
2. Did you then (a) re-run tleap to build a new system; and (b) re-run
cpptraj check to re-check for bad contacts?
A guess: if you just removed certain hydrogen atoms (say), they will get
re-built by tleap (in the same manner as they were in your initial run.)
That doesn't get you anywhere. You will need to genuinely move some atoms
to better locations.
>
>Now, when I check the structure, atom 6514 (HB2) is not overlapping with
>anything! The closest non-bonded atom is at 1.2 Ang (fig attached). Then
>what is the source of this error and how should I avoid this further? Is it
>due to the charges?
The GMAX value just prints the largest element of the force vector. But if
some of the elements are NaN (as in your case), this information is not of
much use, since NaN's are ignored in the search for the maximum value
(but not in the RMS calculation.)
...good luck...dac
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Received on Wed Jun 07 2023 - 05:30:02 PDT
