[gmx-users] Small molecule parametrization
sun.iba2
sun.iba2 at gmail.com
Fri Sep 9 14:21:36 CEST 2016
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.
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<div>-------- Original message --------</div><div>From: Justin Lemkul <jalemkul at vt.edu> </div><div>Date:09/09/2016 5:18 AM (GMT+05:30) </div><div>To: gmx-users at gromacs.org </div><div>Cc: </div><div>Subject: Re: [gmx-users] Small molecule parametrization </div><div>
</div>
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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