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)D1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-1
Forcefieldmultiple
Molecule ID17177
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:14
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 
1731 None - 74 0 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17415 None - 24 1 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
574 None - 17 0 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17413 None - 24 1 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
572 None - 17 0 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17411 None - 18 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17443 None - 28 1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
570 None - 11 0 Manual* N/A Compare with
5182 None - 110 -8 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)