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)RMC
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms30
Net Charge1
Forcefieldmultiple
Molecule ID17335
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:16
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 >
163 None - 13 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
568 None - 16 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
570 None - 11 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
572 None - 17 0 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
574 None - 17 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
576 None - 26 0 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
581 None - 16 0 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
619 None - 16 0 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1589 None - 131 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)