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 building block
Residue Name (RNME)RMA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms33
Net Charge1
Forcefieldmultiple
Molecule ID17148
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 12:55:23
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 
569 None - 8 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17535 None - 24 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)