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) 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)PGA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge-1
Forcefieldmultiple
Molecule ID17258
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:15
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 
570 None - 11 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17216 None - 29 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)