AMBER Archive (2005)

Subject: Re: AMBER: RESP problem RESP

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Nov 14 2005 - 08:59:12 CST

Quoting laura zan <laura_zan75_at_yahoo.com>:

Yes you have diff. between your data & parm94 which are too big...

- Do you have a particular reason to use iop(6/42=6) ?
See the Gaussian input automatically generated by R.E.D.:
#P HF/6-31G* SCF(Conver=6) NoSymm Test Pop=mk IOp(6/33=2)
See also
http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/iops98.htm

- Be aware that you use a different strategy (Me-derivative) than that used in
the Cornell et al FF (DMP + 4 nucleosides). This should slightly increase the
diff. but not that much: How big is the difference with or without this
intra-molecular restraint using your methyl-derivative ? Did you compare the 2
sets of charges ?

> I did a RESP fit on guanine (RG), capped with a methyl
> group at N9. I knew I wouldn't get the same charges as
> those in all_nuc94.in, but I wasn't expecting such big
> differences:
>
> atom all_nuc94.in my charges
> ----------------------------------
> N9 0.0492 -0.008536
> C8 0.1374 0.119023
> H8 0.1640 0.152369
> N7 -0.5709 -0.529202
> C5 0.1744 -0.031449
> C6 0.4770 0.737717
> O6 -0.5597 -0.586775
> N1 -0.4787 -0.819068 !!!
> H1 0.3424 0.416906
> C2 0.7657 1.041551 !!!
> N2 -0.9672 -1.120108 !!!
> H21 0.4364 0.468264
> H22 0.4364 0.468264
> N3 -0.6323 -0.771436
> C4 0.1222 0.358782
> ----------------------------------
> total -0.1037 -0.1037
>
> The total charge on the methyl group was constrained
> at 0.1037, which made the net charge on the base the
> same as that in all_nuc94.in. It is said that
> differences bigger than 0.1 are likely due to errors
> in the inputs, so I am including the gaussian input
> file along with the resp input files (input files were
> generated by antechamber, I modified the RESP inputs
> to add the charge constraint).

Error in the inputs and/or different minima used and/or, ... and/or ...

> Gaussian:
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2)
> iop(6/42=6)

Why do you use iop(6/42=6) ?
This will generate a huge number of MEP points...

> The structure is already optimized
>
> 0 1
> N 2.055470 .915786 .000000
> C .686292 .773862 .000000
> C .343048 -.552488 .000000
> N 1.509766 -1.236982 .000000
> C 2.500180 -.282756 .000000
> C -.359250 1.755612 .000000
> N -1.620822 1.108796 .000000
> C -1.837352 -.233152 .000000
> N -.890976 -1.112274 .000000
> N -3.122779 -.639015 .000000
> O -.322786 2.949160 .000000
> H -3.302019 -1.615975 .000000
> H -3.888045 -.008030 .000000
> H -2.393892 1.739352 .000000
> H 3.534084 -.563481 .000000
> C 1.664508 -2.674579 .000000
> H 1.206542 -3.105048 .880243
> H 1.206542 -3.105048 -.880243
> H 2.719909 -2.908217 .000000

Personnally, I always start from the QM Geometry optimization output, input of
R.E.D. This avoid copy/cut errors in the Cartesian Coordinates...

Moreover, the atom order is different than that reported above ?
How can we know which hydrogen is linked to which heavy atom ?
(This is a problem for the NH2 (& CH3) group, in particular).

> RESP1:
> Resp charges for organic molecule
>
> &cntrl
>
> nmol = 1,
> ihfree = 1,
> ioutopt = 1,
>
> &end
> 1.0
> Resp charges for organic molecule
> 0 19
> 7 0
> 6 0
> 6 0
> 7 0
> 6 0
> 6 0
> 7 0
> 6 0
> 7 0
> 7 0
> 8 0
> 1 0
> 1 12
> 1 0
> 1 0
> 6 0
> 1 0
> 1 0
> 1 0
> 4 0.1037
> 1 16 1 17 1 18 1 19
>
> RESP2:
> Resp charges for organic molecule
>
> &cntrl
>
> nmol = 1,
> ihfree = 1,
> ioutopt = 1,
> iqopt = 2,
> qwt = 0.001,
>
> &end
> 1.0
> Resp charges for organic molecule
> 0 19
> 7 -99
> 6 -99
> 6 -99
> 7 -99
> 6 -99
> 6 -99
> 7 -99
> 6 -99
> 7 -99
> 7 -99
> 8 -99
> 1 -99
> 1 -99
> 1 -99
> 1 -99
> 6 0
> 1 0
> 1 17
> 1 17
> 4 0.1037
> 1 16 1 17 1 18 1 19
>
> I really don't know what's going on, surely there must
> be a mistake somewhere. Please I need your help. I
> would be most grateful if you could help me sort this
> problem out, any suggestion you could give me would be
> highly appreciated. Thank you.

Regards, Francois

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