Re: [AMBER] RESP charges for iron-sulfur cluster

From: safwat abdel-azeim <safwatazeim.gmail.com>
Date: Mon, 11 Mar 2013 14:57:59 +0300

Hi Francesco,
Many thanks for your message, but I wanted to understand what this happens
with antechamber. Actually I used ONIOM to study the relativity of my
enzyme which uses iron-sulfur cluster as co-factor to reduce a substrate.
the coordinates of the active site is attached. I would like to study the
hydrogen bond net work around the cluster using MD which is important for
the reactivity.

Best regards,
Safwat




On Mon, Mar 11, 2013 at 1:29 PM, francesco oteri
<francesco.oteri.gmail.com>wrote:

> Hi Safwat,
> I don't know exactly your system. But if you are interested in FeS cluster
> there is this paper
> where they have been parametrised
> http://pubs.acs.org/doi/abs/10.1021/ct300185u
>
>
> Francesco
>
> 2013/3/11 safwat abdel-azeim <safwatazeim.gmail.com>
>
> > Dear All,
> > I am calculating RESP charges using Antechamber of iron-sulfur cluster
> > complex. I used BS-DFT to optimize the geometry and UHF/6-31G* to
> > calculate ESP with the same wave function. But when I used antechamber
> > to get RESP charges using the following commands, it gave totally
> > different charges, for ex. for Phosphorus it changes from positive to
> > negative. I used g03 to generate ESP and Amber12. Can you help me to
> > figure out this error. Why when I used Mol2 and PDB output file
> > format the results are different.
> >
> > Case-1- antechamber -i isph_BS2_ESP.log -fi gout -o
> > isph_BS2_charges.mol2 -fo mol2 -c resp -nc -3 -m 1 -j 0
> >
> > Case-2- antechamber -i isph_BS2_ESP.log -fi gout -o
> > isph_BS2_charges.pdb -fo pdb -c resp -nc -3 -m 1 -j 0
> >
> >
> > case-1 case-2
> > 1 H1 -2.7348 5.7385 -0.8702 H1 1 MOL
> > 0.033219 -0.022303
> > 2 C1 -2.5036 4.6673 -1.0416 C1 1 MOL
> > -0.006299 0.223724
> > 3 H2 -3.4415 4.1405 -1.2117 H2 1 MOL
> > 0.033219 -0.022303
> > 4 H3 -1.9101 4.5871 -1.9546 H3 1 MOL
> > 0.033219 -0.022303
> > 5 S1 -1.6066 3.8893 0.3720 S1 1 MOL
> > -0.707521 -0.800886
> > 6 H4 -3.3050 -1.4034 5.5582 H4 1 MOL
> > 0.033219 -0.022303
> > 7 C2 -2.9799 -1.2191 4.5082 C2 1 MOL
> > -0.006299 0.223724
> > 8 H5 -2.3867 -0.3060 4.4967 H5 1 MOL
> > 0.033219 -0.022303
> > 9 H6 -2.3121 -2.0323 4.2283 H6 1 MOL
> > 0.033219 -0.022303
> > 10 S2 -4.3120 -1.1069 3.2118 S2 1 MOL
> > -0.707521 -0.800886
> > 11 H7 -5.1424 -2.6200 -4.3101 H7 1 MOL
> > 0.033219 -0.022303
> > 12 C3 -4.8240 -2.0589 -3.4127 C3 1 MOL
> > -0.006299 0.223724
> > 13 H8 -5.6519 -1.4230 -3.0942 H8 1 MOL
> > 0.033219 -0.022303
> > 14 H9 -4.6241 -2.7705 -2.6120 H9 1 MOL
> > 0.033219 -0.022303
> > 15 S3 -3.3258 -1.0246 -3.7285 S3 1 MOL
> > -0.707521 -0.800886
> > 16 C4 1.6353 -2.2124 1.1152 C4 1 MOL
> > 0.347237 0.223724
> > 17 O1 0.9116 -2.2227 -0.1518 O1 1 MOL
> > -0.700173 -0.302119
> > 18 C5 2.2372 -0.7879 1.2410 C5 1 MOL
> > -0.071025 0.223724
> > 19 C6 2.3257 0.0024 0.1730 C6 1 MOL
> > 0.086187 0.223724
> > 20 C7 2.8221 1.4245 0.2108 C7 1 MOL
> > 0.060883 0.223724
> > 21 O2 3.9728 1.6405 -0.5892 O2 1 MOL
> > -0.524297 -0.302119
> > 22 P1 5.4882 1.4598 0.1036 P1 1 MOL
> > 1.268858 -0.137089
> > 23 O3 5.5282 -0.1673 0.3453 O3 1 MOL
> > -0.584555 -0.302119
> > 24 P2 6.1049 -1.3333 -0.6581 P2 1 MOL
> > 1.447997 -0.137089
> > 25 O4 5.1335 -2.6035 -0.1127 O4 1 MOL
> > -0.810740 -0.302119
> > 26 O5 7.5113 -1.6974 -0.2624 O5 1 MOL
> > -0.860675 -0.302119
> > 27 O6 5.7280 -1.0215 -2.0787 O6 1 MOL
> > -0.860675 -0.302119
> > 28 O7 5.4889 2.0252 1.5043 O7 1 MOL
> > -0.816971 -0.302119
> > 29 O8 6.4606 1.8761 -0.9688 O8 1 MOL
> > -0.816971 -0.302119
> > 30 C8 2.7089 -0.2368 2.5772 C8 1 MOL
> > -0.328186 0.223724
> > 31 H10 2.4023 -2.9928 1.1206 H10 1 MOL
> > 0.033638 -0.022303
> > 32 H11 0.9627 -2.4548 1.9504 H11 1 MOL
> > 0.033638 -0.022303
> > 33 H12 0.2705 -2.8033 0.4650 H12 1 MOL
> > 0.244208 -0.022303
> > 34 H13 2.0713 -0.3784 -0.8125 H13 1 MOL
> > 0.095202 -0.022303
> > 35 H14 2.0295 2.0676 -0.1968 H14 1 MOL
> > 0.115549 -0.022303
> > 36 H15 2.9883 1.7554 1.2434 H15 1 MOL
> > 0.115549 -0.022303
> > 37 H16 3.4730 0.5221 2.4322 H16 1 MOL
> > 0.096618 -0.022303
> > 38 H17 1.8969 0.2258 3.1623 H17 1 MOL
> > 0.096618 -0.022303
> > 39 H18 3.1366 -1.0374 3.1853 H18 1 MOL
> > 0.096618 -0.022303
> > 40 H19 4.2060 -2.3440 -0.2118 H19 1 MOL
> > 0.377654 -0.022303
> > 41 Fe1 -1.8353 1.6678 -0.0293 Fe1 1 MOL
> > 1.044820 0.982822
> > 42 Fe2 -0.5794 -0.8762 0.0259 Fe2 1 MOL
> > 1.044820 0.982822
> > 43 Fe3 -2.7635 -0.4471 -1.5904 Fe3 1 MOL
> > 1.044820 0.982822
> > 44 Fe4 -3.1684 -0.5310 1.2806 Fe4 1 MOL
> > 1.044820 0.982822
> > 45 S4 -0.7199 0.6552 -1.8014 S4 1 MOL
> > -0.869744 -0.800886
> > 46 S5 -2.5692 -2.2740 -0.1602 S5 1 MOL
> > -0.869744 -0.800886
> > 47 S6 -1.0930 0.4782 1.8149 S6 1 MOL
> > -0.869744 -0.800886
> > 48 S7 -4.0748 1.0308 -0.3227 S7 1 MOL
> > -0.869744 -0.800886
> >
> > The spin densities in case of DFT-B3lyp
> > 41 Fe -4.814404
> > 42 Fe -4.555871
> > 43 Fe 4.669129
> > 44 Fe 4.644358
> > The spin densities in case of UHF
> > 41 Fe -4.664168
> > 42 Fe -4.008851
> > 43 Fe 4.026178
> > 44 Fe 4.694864
> >
> > Best regards,
> > Safwat
> >
> >
> >
> >
> >
> >
> > --
> > -----------------------------------------------------------
> > Safwat Abdel-Azeim, PhD
> > Computational Chemistry (Modeling of Biomolecules)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
-----------------------------------------------------------
Safwat Abdel-Azeim, PhD
Computational Chemistry (Modeling of Biomolecules)



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Mon Mar 11 2013 - 05:30:02 PDT
Custom Search