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Molecular dynamic simulation of alkaloids
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0
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153
|
March 2, 2024
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PACKMOL and gmx2pdb
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0
|
280
|
February 20, 2024
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Inserting a modified residue into a protein/DNA chain using pdb2gmx
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18
|
1092
|
February 17, 2024
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Overiding bonded parameters from ffbonded.itp by explicitly specifying in residue.rtp
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0
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195
|
February 16, 2024
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Urgent: Queries regarding the gromacs file synthesis for DNA-lipid systems
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5
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239
|
February 15, 2024
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Atom not recognized, but clearly is in the pdb [pdb2gmx using Charmm36]
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3
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296
|
February 14, 2024
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Fatal error: Atom HO2' in residue A 21 was not found in rtp entry ADE with 31 atoms while sorting
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1
|
263
|
February 6, 2024
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Fatal error: number of coordinates in coordinate file does not match topology file
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2
|
651
|
February 3, 2024
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Fatal Error atom C2 not found in building block 465MET while combining tdb and rtp
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1
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200
|
January 28, 2024
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How can I generate a toplogy from a pdb file with non-standard residues?
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1
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185
|
January 25, 2024
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Loading a Ecoli Ribosome structure in Gromacs 6i0y/4v7u
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2
|
165
|
January 24, 2024
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Pdb2gmx does not recognize disulfides accurately
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3
|
535
|
January 5, 2024
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Protonation/disulfide issues with pdb2gmx?
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2
|
399
|
January 5, 2024
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Fatal error while running gromacs. Atom N not found in building block 1DG while combining tdb &rtp
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1
|
195
|
January 3, 2024
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How to include a itp file to gromacs forcefiled
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5
|
596
|
January 2, 2024
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|
Grmacs_Drude
|
|
14
|
350
|
December 15, 2023
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Atom P in residue DA 90 was not found in rtp entry DA5 with 30 atoms while sorting atoms
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|
9
|
566
|
November 20, 2023
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|
Rtp conversion charmm36
|
|
1
|
503
|
November 17, 2023
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LINCS WARNING (but with atom duplication)
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2
|
234
|
October 27, 2023
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Force fields
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0
|
265
|
October 21, 2023
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.rtp file generation
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0
|
214
|
October 16, 2023
|
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Covalent bond between protein and ligand (cobalamin)
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|
4
|
731
|
October 5, 2023
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Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms while sorting atoms
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|
3
|
1010
|
October 1, 2023
|
|
Error in running pdb2gmx for protein with modified residue
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|
1
|
334
|
September 30, 2023
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Generating PDB file for custom DNA sequence?
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0
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287
|
September 27, 2023
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Error: atom C1 not found in buiding block 1MET while combining tdb and rtp
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|
2
|
1004
|
September 26, 2023
|
|
Protein-specific termini
|
|
1
|
361
|
September 15, 2023
|
|
Hybrid molecule topologies for intermolecular distance restraints
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|
1
|
235
|
August 18, 2023
|
|
Error in conversion of pdb file to gro file
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|
0
|
286
|
August 13, 2023
|
|
Md simulation
|
|
1
|
220
|
August 9, 2023
|