Peter, thanks for explanations!
Could you tell me is it possible to convert CGenFF output for hetatomic group to the RTP (not an itp ) gromac's data ? I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein which is consist of HETTATOMIC chromophore covently bonded to the polypeptide chain of that protein so I need topology for that chromophore ( I can make it by swiss param or my CGenFF) but I need that topology in the rtp file format to integrate it to the aminoacids.rtp of the Charmm27 for further processing of the entirely GFP by means of pdb2gmx. 2012/12/8, Peter C. Lai <p...@uab.edu>: > On 2012-12-08 03:20:54AM -0800, James Starlight wrote: >> 1- on what assumptions that blocks were generated ? > > This appears to be a swissparm-specific question. I don't know what > algorithms it uses to match what are essentially pharmacophores in the new > molecule with the common individual blocks it finds. > >> 2- Why charge in [ atomtypes ] (zero) differes from the charges in > > Because gromacs ignores charges in [atomtypes], so the easiest thing is to > just assign all zeros to that column. > >> the topology of the same groups? how I can check correctness of charge >> distribution in such itp files ? > > Compare to analogous molecules and see if there are published charges. > You can also use the building blocks and manually assign charges and see > what > you end up with as well. To be totally rigorous, parameterize the structure > > using a quantum chemistry package and compare the ab initio charge > distributions to the ones assigned by SwissParm (or by hand). > >> 3- What is sigma and epsilon in the [ atomtypes ] ? :) > > LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1 > >> 4- Have anybody else used Swiss param for modeling protein-ligands >> systems? Might it be used with the charmm36 set ? >> > > CHARMM has its own generalized forcefield (CGenFF) for ligands and other > molecules, although charmm36 may have cAMP in their nucleotides section... > You can try to also build it using adenine, ribose, and add phosphate. > > CGenFF and C36 are interoperable for intermolecular interactions, so if > using CGenFF to paramterize cAMP you would use ParamChem to assign charges > and then convert and add the CGenFF forcefield parameters (from the gromacs > contributions website) to C36. There are mailing list archives that show > you the script to use to do the CGenFF conversion. > > > >> James >> >> 2012/12/7, Justin Lemkul <jalem...@vt.edu>: >> > >> > >> > On 12/7/12 2:21 PM, James Starlight wrote: >> >> Justin, >> >> >> >> with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 >> >> rvdw=1.2 >> >> rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp >> >> >> >> NOTE 1 [file ./mdps/em.mdp]: >> >> For energy conservation with switch/shift potentials, rlist should >> >> be >> >> 0.1 >> >> to 0.3 nm larger than rvdw. >> >> >> >> NOTE 2 [file ./mdps/em.mdp]: >> >> The sum of the two largest charge group radii (0.078024) is larger >> >> than >> >> rlist (1.200000) - rvdw (1.200000) >> >> >> > >> > As I recall, there is a small bug where grompp ignores rlistlong when >> > printing >> > this message. The simulation will be fine. >> > >> > -Justin >> > >> >> >> >> Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same >> >> value because of PME) ? >> >> >> >> 2012/12/7, Justin Lemkul <jalem...@vt.edu>: >> >>> >> >>> >> >>> On 12/7/12 1:19 PM, James Starlight wrote: >> >>>> Justin, >> >>>> >> >>>> following to your advise I've tried to use charmm 27 ff for >> >>>> simulation >> >>>> of my protein-cGMP complex ( ligand was parametrized by Swiss Param >> >>>> server). >> >>>> >> >>>> Could you provide me with the cut-offs for vdw as well as >> >>>> electrostatics suitable for simulation in charmm27 and 36 force >> >>>> fields? >> >>>> >> >>> >> >>> http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html >> >>> >> >>>> Does anybody know another servers for parametrization of the ligands >> >>>> for charmm simulation in gromacs? >> >>>> >> >>> >> >>> If Google can't find it, it probably doesn't exist. >> >>> >> >>> -Justin >> >>> >> >>>> 2012/12/7, Justin Lemkul <jalem...@vt.edu>: >> >>>>> >> >>>>> >> >>>>> On 12/7/12 11:42 AM, James Starlight wrote: >> >>>>>> Justin, >> >>>>>> >> >>>>>> ligand-only simulation in vacuum have been finished with the same >> >>>>>> errors >> >>>>>> :) >> >>>>>> >> >>>>>> Step 19200, time 38.4 (ps) LINCS WARNING >> >>>>>> relative constraint deviation after LINCS: >> >>>>>> rms 0.025443, max 0.140660 (between atoms 1 and 3) >> >>>>>> bonds that rotated more than 30 degrees: >> >>>>>> atom 1 atom 2 angle previous, current, constraint length >> >>>>>> 1 2 52.2 0.1033 0.0985 0.1000 >> >>>>>> 1 3 90.1 0.1168 0.1141 0.1000 >> >>>>>> >> >>>>>> Step 19200, time 38.4 (ps) LINCS WARNING >> >>>>>> relative constraint deviation after LINCS: >> >>>>>> rms 0.025376, max 0.140474 (between atoms 1 and 3) >> >>>>>> bonds that rotated more than 30 degrees: >> >>>>>> atom 1 atom 2 angle previous, current, constraint length >> >>>>>> 1 2 52.0 0.1033 0.0988 0.1000 >> >>>>>> 1 3 90.0 0.1168 0.1140 0.1000 >> >>>>>> step 19200, will finish Sat Dec 8 04:10:49 2012 >> >>>>>> Step 19201, time 38.402 (ps) LINCS WARNING >> >>>>>> relative constraint deviation after LINCS: >> >>>>>> rms 0.052715, max 0.293316 (between atoms 1 and 3) >> >>>>>> bonds that rotated more than 30 degrees: >> >>>>>> atom 1 atom 2 angle previous, current, constraint length >> >>>>>> 1 2 49.3 0.0988 0.0993 0.1000 >> >>>>>> 1 3 90.0 0.1140 0.1293 0.1000 >> >>>>>> >> >>>>>> Step 19201, time 38.402 (ps) LINCS WARNING >> >>>>>> relative constraint deviation after LINCS: >> >>>>>> rms 0.052900, max 0.294281 (between atoms 1 and 3) >> >>>>>> bonds that rotated more than 30 degrees: >> >>>>>> atom 1 atom 2 angle previous, current, constraint length >> >>>>>> 1 2 49.6 0.0988 0.0989 0.1000 >> >>>>>> 1 3 90.0 0.1140 0.1294 0.1000 >> >>>>>> >> >>>>>> Step 19202, time 38.404 (ps) LINCS WARNING >> >>>>>> relative constraint deviation after LINCS: >> >>>>>> rms 0.035783, max 0.198482 (between atoms 1 and 3) >> >>>>>> bonds that rotated more than 30 degrees: >> >>>>>> atom 1 atom 2 angle previous, current, constraint length >> >>>>>> 1 2 33.3 0.0989 0.0984 0.1000 >> >>>>>> 1 3 89.9 0.1294 0.1198 0.1000 >> >>>>>> >> >>>>>> ------------------------------------------------------- >> >>>>>> Program mdrun, VERSION 4.5.4 >> >>>>>> Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176 >> >>>>>> >> >>>>>> Fatal error: >> >>>>>> Too many LINCS warnings (1000) >> >>>>>> >> >>>>>> >> >>>>>> ITs intresting that the same files (like step-1c_n11.pdb) have >> >>>>>> been >> >>>>>> produced already during CG minimisation phase but the system have >> >>>>>> not >> >>>>>> been crashed. So I suppoe that the problem is in geometry of the >> >>>>> >> >>>>> If you get errors in the minimization, that should indicate that >> >>>>> either >> >>>>> the >> >>>>> >> >>>>> topology or configuration is flawed. >> >>>>> >> >>>>>> mollecule. The direct comparison of the bonds and angles with the >> >>>>>> rtp >> >>>>>> (DGUA) is non trivial again because of differs in the file formats >> >>>>>> representation :) >> >>>>>> >> >>>>> >> >>>>> Most troubleshooting is not easy. You can also create a topology >> >>>>> for >> >>>>> DGUA >> >>>>> from >> >>>>> just about any DNA structure and compare its .top against your cGMP >> >>>>> topology. >> >>>>> >> >>>>> -Justin >> >>>>> >> >>>>> -- >> >>>>> ======================================== >> >>>>> >> >>>>> Justin A. Lemkul, Ph.D. >> >>>>> Research Scientist >> >>>>> Department of Biochemistry >> >>>>> Virginia Tech >> >>>>> Blacksburg, VA >> >>>>> jalemkul[at]vt.edu | (540) 231-9080 >> >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >>>>> >> >>>>> ======================================== >> >>>>> -- >> >>>>> gmx-users mailing list gmx-users@gromacs.org >> >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >>>>> * Please search the archive at >> >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >>>>> * Please don't post (un)subscribe requests to the list. Use the >> >>>>> www interface or send it to gmx-users-requ...@gromacs.org. >> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>>>> >> >>> >> >>> -- >> >>> ======================================== >> >>> >> >>> Justin A. Lemkul, Ph.D. >> >>> Research Scientist >> >>> Department of Biochemistry >> >>> Virginia Tech >> >>> Blacksburg, VA >> >>> jalemkul[at]vt.edu | (540) 231-9080 >> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >>> >> >>> ======================================== >> >>> -- >> >>> gmx-users mailing list gmx-users@gromacs.org >> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >>> * Please search the archive at >> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >>> * Please don't post (un)subscribe requests to the list. Use the >> >>> www interface or send it to gmx-users-requ...@gromacs.org. >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> > >> > -- >> > ======================================== >> > >> > Justin A. Lemkul, Ph.D. >> > Research Scientist >> > Department of Biochemistry >> > Virginia Tech >> > Blacksburg, VA >> > jalemkul[at]vt.edu | (540) 231-9080 >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> > ======================================== >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > * Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
