MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 2000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeamino acid
Residue Name (RNME)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17545
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:19
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (1-100 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
18675 None - 140 -3 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
570 None - 11 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17161 None - 23 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17163 None - 23 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
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ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)