Today I've made parametrization of the chromophore group by means of Swiss param and integrated that topology into charmm27 ff. The only problem that I have is with the N-term N atom of the chromophore. It's likely that I made mistake to parametrize it into full protonated form (NH2).
When I've used pdb2gmx on the GFP structure the peptide bond between that N atom and adjacent O ( from C term of adjacent residue) is incorrect ( both oxygens preserves on the C atom so my system had divided onto 2 chains as well as had incorrect charge). How I could define the N atom in the topology as the N-terminal? (I've delited both hydrogens from RTP as well as from HDB files but the problem didn’t resolved. Also I'm using -ignh on the input pdb to ignore all hydrogens from the model) James 2012/12/11, Justin Lemkul <jalem...@vt.edu>: > > > On 12/11/12 6:04 AM, James Starlight wrote: >> 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. >> > > You've repeated this request several times now, and the answer is always the > > same. If you have suitable parameters in some form, they need to be > converted > to Gromacs format (.rtp) by some means. If you haven't found or written > some > program that converts the formats, the only solution is to fire up your > favorite > text editor, open up the Gromacs manual, and get typing. The .rtp format is > > relatively straightforward, and you will probably be better served if you > try to > write one and post back with specific questions if you have specific > problems > getting it to work. > > Note that suitable parameters for the GFP chromophore are published (and > that > paper was linked before in this discussion), so you likely do not need to > re-derive any of these parameters using SwissParam or CGenFF. A few years > ago, > we used the published CHARMM27-compatible parameters in a set of GFP > simulations. > > -Justin > >> 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 >>> > > -- > ======================================== > > Justin A. 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