MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

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) 1000 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)PYA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms9
Net Charge-1
Forcefieldmultiple
Molecule ID17296
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS11 Files

Topology Files Structure Files
GROMOS11 United-Atom MTB
United-Atom PDB (optimised geometry)

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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17458 None - 28 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17173 None - 25 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17474 None - 23 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17181 None - 23 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17482 None - 15 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17514 None - 26 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
Previous Page Next Page

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)