[gmx-users] Small molecule parametrization
Sun Iba
sun.iba2 at gmail.com
Fri Sep 9 14:33:56 CEST 2016
Justin please have look at PDB coordinates:
HEADER UNCLASSIFIED 08-Sep-16
TITLE UNITED ATOM STRUCTURE FOR MOLECULE UNK
AUTHOR GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2016-09-05 10:31:24
AUTHOR 2 http://compbio.biosci.uq.edu.au/atb
HETATM 1 C12 SCX1 0 -1.450 -4.041 -0.077 1.00 0.00 C
HETATM 2 O1 SCX1 0 -2.719 -3.434 -0.134 1.00 0.00 O
HETATM 3 C3 SCX1 0 -2.815 -2.071 -0.157 1.00 0.00 C
HETATM 4 C2 SCX1 0 -4.079 -1.455 -0.012 1.00 0.00 C
HETATM 5 C4 SCX1 0 -1.693 -1.233 -0.290 1.00 0.00 C
HETATM 6 H2 SCX1 0 -0.689 -1.664 -0.419 1.00 0.00 H
HETATM 7 C6 SCX1 0 -5.387 -2.138 0.065 1.00 0.00 C
HETATM 8 H4 SCX1 0 -6.255 -1.451 0.117 1.00 0.00 H
HETATM 9 C9 SCX1 0 -5.767 -3.438 0.069 1.00 0.00 C
HETATM 10 C13 SCX1 0 -7.246 -3.703 0.131 1.00 0.00 C
HETATM 11 N2 SCX1 0 -8.455 -3.909 0.168 1.00 0.00 N
HETATM 12 C19 SCX1 0 -4.965 -4.688 0.013 1.00 0.00 C
HETATM 13 N4 SCX1 0 -4.368 -5.763 -0.028 1.00 0.00 N
HETATM 14 C1 SCX1 0 -4.139 -0.046 0.045 1.00 0.00 C
HETATM 15 H1 SCX1 0 -5.107 0.471 0.159 1.00 0.00 H
HETATM 16 C5 SCX1 0 -3.004 0.756 -0.044 1.00 0.00 C
HETATM 17 H3 SCX1 0 -3.100 1.853 0.003 1.00 0.00 H
HETATM 18 C7 SCX1 0 -1.760 0.161 -0.251 1.00 0.00 C
HETATM 19 C11 SCX1 0 -0.521 0.988 -0.408 1.00 0.00 C
HETATM 20 H6 SCX1 0 -0.024 1.023 -1.390 1.00 0.00 H
HETATM 21 N1 SCX1 0 0.002 1.677 0.531 1.00 0.00 N
HETATM 22 N3 SCX1 0 1.409 2.643 0.125 1.00 0.00 N
HETATM 23 C16 SCX1 0 1.077 4.001 0.074 1.00 0.00 C
HETATM 24 O2 SCX1 0 1.893 4.908 0.253 1.00 0.00 O
HETATM 25 C18 SCX1 0 -0.392 4.495 -0.144 1.00 0.00 C
HETATM 26 F1 SCX1 0 -0.916 4.834 1.027 1.00 0.00 F
HETATM 27 F2 SCX1 0 -0.433 5.577 -0.910 1.00 0.00 F
HETATM 28 F3 SCX1 0 -1.192 3.601 -0.695 1.00 0.00 F
HETATM 29 C15 SCX1 0 2.780 2.075 0.077 1.00 0.00 C
HETATM 30 C14 SCX1 0 3.094 0.702 0.223 1.00 0.00 C
HETATM 31 C10 SCX1 0 2.068 -0.383 0.443 1.00 0.00 C
HETATM 32 C22 SCX1 0 4.428 0.269 0.163 1.00 0.00 C
HETATM 33 H11 SCX1 0 4.661 -0.804 0.260 1.00 0.00 H
HETATM 34 C21 SCX1 0 5.509 1.132 -0.017 1.00 0.00 C
HETATM 35 C8 SCX1 0 6.926 0.616 -0.050 1.00 0.00 C
HETATM 36 C20 SCX1 0 5.211 2.486 -0.157 1.00 0.00 C
HETATM 37 H10 SCX1 0 6.028 3.213 -0.295 1.00 0.00 H
HETATM 38 C17 SCX1 0 3.887 2.924 -0.131 1.00 0.00 C
HETATM 39 H8 SCX1 0 3.778 4.005 -0.281 1.00 0.00 H
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4 5
CONECT 4 3 7 14
CONECT 5 3 6 18
CONECT 6 5
CONECT 7 4 8 9
CONECT 8 7
CONECT 9 7 10 12
CONECT 10 9 11
CONECT 11 10
CONECT 12 9 13
CONECT 13 12
CONECT 14 4 15 16
CONECT 15 14
CONECT 16 14 17 18
CONECT 17 16
CONECT 18 5 16 19
CONECT 19 18 20 21
CONECT 20 19
CONECT 21 19 22
CONECT 22 21 23 29
CONECT 23 22 24 25
CONECT 24 23
CONECT 25 23 26 27 28
CONECT 26 25
CONECT 27 25
CONECT 28 25
CONECT 29 22 30 38
CONECT 30 29 31 32
CONECT 31 30
CONECT 32 30 33 34
CONECT 33 32
CONECT 34 32 35 36
CONECT 35 34
CONECT 36 34 37 38
CONECT 37 36
CONECT 38 29 36 39
CONECT 39 38
END
On Fri, Sep 9, 2016 at 5:51 PM, sun.iba2 <sun.iba2 at gmail.com> wrote:
> This is a small molecule with dicyanovinyl group substituted at para
> position on one of the phenyl ring. I suspect the charges are not proper
> because in ATB the group charges must be -1,0 or 1. For some groups charges
> are summed up to zero but this is not the case of all groups.
>
>
> Sent from Samsung Mobile
>
>
> -------- Original message --------
> From: Justin Lemkul <jalemkul at vt.edu>
> Date:09/09/2016 5:18 AM (GMT+05:30)
> To: gmx-users at gromacs.org
> Cc:
> Subject: Re: [gmx-users] Small molecule parametrization
>
>
>
> On 9/7/16 1:43 PM, Sun Iba wrote:
> > Hi
> > I have parametreized my small molecule with the help of ATB server. I
> have
> > learnt that ATB provides GROMOS charges better than PRODRG. However, I
> have
> > serious doubts regarding the charges assigned to hydrophobic groups.
> Also I
> > need to convert the calculated charges into GROMOS 43a1 set (force field
> I
> > am using). I am pasting the .itp file produced by ATB:
> >
> > nr type resnr resid atom cgnr charge mass total_charge
> > 1 CH3 1 SCX1 C12 1 0.223 15.0350
> > 2 OE 1 SCX1 O1 1 -0.275 15.9994 ; -0.052
> > 3 C 1 SCX1 C3 2 0.476 12.0110
> > 4 C 1 SCX1 C2 2 -0.157 12.0110
> > 5 C 1 SCX1 C4 2 -0.376 12.0110
> > 6 HC 1 SCX1 H2 2 0.172 1.0080 ; 0.115
> > 7 C 1 SCX1 C6 3 0.095 12.0110
> > 8 HC 1 SCX1 H4 3 0.137 1.0080
> > 9 C 1 SCX1 C9 3 -0.386 12.0110
> > 10 C 1 SCX1 C13 3 0.478 12.0110
> > 11 NR 1 SCX1 N2 3 -0.525 14.0067 ; -0.201
> > 12 C 1 SCX1 C19 4 0.539 12.0110
> > 13 NR 1 SCX1 N4 4 -0.539 14.0067 ; 0.000
> > 14 C 1 SCX1 C1 5 -0.117 12.0110
> > 15 HC 1 SCX1 H1 5 0.157 1.0080
> > 16 C 1 SCX1 C5 5 -0.150 12.0110
> > 17 HC 1 SCX1 H3 5 0.131 1.0080 ; 0.021
> > 18 C 1 SCX1 C7 6 0.097 12.0110
> > 19 C 1 SCX1 C11 6 0.247 12.0110
> > 20 HC 1 SCX1 H6 6 0.079 1.0080
> > 21 NR 1 SCX1 N1 6 -0.423 14.0067 ; 0.000
> > 22 NT 1 SCX1 N3 7 0.171 14.0067
> > 23 C 1 SCX1 C16 7 0.387 12.0110
> > 24 O 1 SCX1 O2 7 -0.492 15.9994
> > 25 C 1 SCX1 C18 7 0.495 12.0110
> > 26 F 1 SCX1 F1 7 -0.187 18.9984
> > 27 F 1 SCX1 F2 7 -0.187 18.9984
> > 28 F 1 SCX1 F3 7 -0.187 18.9984 ; 0.000
> > 29 C 1 SCX1 C15 8 -0.211 12.0110
> > 30 C 1 SCX1 C14 8 0.388 12.0110
> > 31 CH3 1 SCX1 C10 8 -0.060 15.0350 ; 0.117
> > 32 C 1 SCX1 C22 9 -0.444 12.0110
> > 33 HC 1 SCX1 H11 9 0.187 1.0080
> > 34 C 1 SCX1 C21 9 0.309 12.0110
> > 35 CH3 1 SCX1 C8 9 -0.052 15.0350 ; 0.000
> > 36 C 1 SCX1 C20 10 -0.340 12.0110
> > 37 HC 1 SCX1 H10 10 0.226 1.0080
> > 38 C 1 SCX1 C17 10 -0.026 12.0110
> > 39 HC 1 SCX1 H8 10 0.140 1.0080 ; 0.000
> >
>
> What is this molecule and why do you think the charges are inappropriate?
>
> >
> > Please have a look and help me understanding if the charges are too bad.
> > Also my Nitrogen atom is not aromatic. It is linked to C by triple bond
> and
> > to another N by double bond. Does GROMOS treat this type of nitrogn as NT
> > and NR?
> >
>
> N can't be linked to one atom via triple bond and another via double bond.
> That's five bonds. Unless your N has expanded its valence into
> d-orbitals,
> that's not going to be possible.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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