[gmx-users] How to reduce the penalty of small molecule from CGenFF

[Justin Lemkul]

On 3/29/20 1:29 AM, Rolly Ng wrote:
> Hello Justin,
> Thank you and yes. I went to the paper and it shows the steps for
> optimization.
> However, I have the following problems as I tried to follow the tutorial on
> CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor
>
> (1) what are these parameters in water_constr.inp? what values should I use
> in my case?
> if @stage eq 4 echo ######## USING MP2 GEOMETRY!!! ########
> echo QM dipole (Debye)
> echo mp2/6-31g*: X=    -3.1938    Y=     1.2595    Z=     0.0011  Tot=
> 3.4332
> echo hf/6-31g*:  X=    -3.4411    Y=     1.3570    Z=     0.0012  Tot=
> 3.6990
>
> (2) How can I get the correct value for the IC table for surface of
> interest? I suppose H2O molecules are placed one at a time to the C and N
> atoms of my molecule but where to place the dummy?
> generate dum first none last none setup warn noangle nodihedral
> join @residue dum renumber
> !preparation of IC table for surface of interest
> ic edit
> dihe 1 N2   1 C1   1 H1   3 dum   0.0
> dihe 1 C1   1 H1   3 dum  4 dum   0.0
> dihe 4 dum  3 dum  1 H1   2 oh2 180.0
> end
> ic fill preserve
> ic edit
> dihe 3 dum  1 H1   2 oh2  2 h1   90.0
> dihe 3 dum  1 H1   2 oh2  2 h2  -90.0
> bond 1 H1   3 dum  1.
> bond 3 dum  4 dum  1.
> bond 1 H1   2 oh2  @d !varied
> bond 2 oh2  2 h1   0.9572
> bond 2 oh2  2 h2   0.9572
> angl 1 C1   1 H1   3 dum  90.0
> angl 1 H1   3 dum  4 dum  90.0
> angl 3 dum  1 H1   2 oh2  90.0
> angl 1 H1   2 oh2  2 h1  127.74
> angl 1 H1   2 oh2  2 h2  127.74
> end
>
> How can I know the bond, angle and dihedral without a GUI show these
> parameters?
>
> Thanks for your patient.
If you have questions about CHARMM, you should use the CHARMM forum.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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