Today I've performed test simulation of the protein-cAMP complex with the charmm27 force field and obtain good stable system. I've compared polar contacts of my complex ( ligand have been done with SwissParam) with the X-ray structure of that protein solved with the same complex and obtained similar picture in both cases. When I've checked ligand's topology produced by Swiss param I noticed that it was built from some building blocks generated by SwissParam ( and found in the same topology file) with the specified charge distribution ( the below example is the cAMP mollecule)
; nr type resnr resid atom cgnr charge mass 1 NPYL 1 LIG N9 1 0.0476 14.0067 2 C5A 1 LIG C8 2 0.0365 12.0110 3 N5B 1 LIG N7 3 -0.5653 14.0067 4 C5B 1 LIG C5 4 0.2272 12.0110 5 CB 1 LIG C6 5 0.4100 12.0110 6 NPYD 1 LIG N1 6 -0.6200 14.0067 7 CB 1 LIG C2 7 0.4700 12.0110 8 NPYD 1 LIG N3 8 -0.5670 14.0067 9 C5A 1 LIG C4 9 0.1054 12.0110 10 HCMM 1 LIG H01 10 0.1500 1.0079 11 HCMM 1 LIG H02 11 0.0000 1.0079 12 HCMM 1 LIG H03 12 0.0000 1.0079 13 HCMM 1 LIG H04 13 0.0000 1.0079 14 HCMM 1 LIG H05 14 0.0000 1.0079 15 HOR 1 LIG H06 15 0.4000 1.0079 16 HCMM 1 LIG H07 16 0.0000 1.0079 17 HCMM 1 LIG H08 17 0.1500 1.0079 18 HNCO 1 LIG H09 18 0.4000 1.0079 19 HNCO 1 LIG H10 19 0.4000 1.0079 20 HCMM 1 LIG H11 20 0.0000 1.0079 21 PO4 1 LIG P 21 1.4424 30.9738 22 O2CM 1 LIG O1P 22 -0.9500 15.9994 23 O2CM 1 LIG O2P 23 -0.9500 15.9994 24 OR 1 LIG O5' 24 -0.5512 15.9994 25 CR 1 LIG C5' 25 0.2800 12.0110 26 CR 1 LIG C4' 26 0.2800 12.0110 27 OR 1 LIG O4' 27 -0.5600 15.9994 28 CR 1 LIG C3' 28 0.2800 12.0110 29 OR 1 LIG O3' 29 -0.5512 15.9994 30 CR 1 LIG C2' 30 0.2800 12.0110 31 OR 1 LIG O2' 31 -0.6800 15.9994 32 CR 1 LIG C1' 32 0.5356 12.0110 33 NC=C 1 LIG N6 33 -0.9000 14.0067 where building blocks were [ atomtypes ] ; name at.num mass charge ptype sigma epsilon NPYL 7 14.0067 0.0 A 0.306469 0.376560 C5A 6 12.0110 0.0 A 0.363487 0.209200 N5B 7 14.0067 0.0 A 0.329632 0.836800 C5B 6 12.0110 0.0 A 0.363487 0.209200 CB 6 12.0110 0.0 A 0.355005 0.292880 NPYD 7 14.0067 0.0 A 0.329632 0.836800 HCMM 1 1.0079 0.0 A 0.235197 0.092048 HOR 1 1.0079 0.0 A 0.040001 0.192464 HNCO 1 1.0079 0.0 A 0.040001 0.192464 PO4 15 30.9738 0.0 A 0.383086 2.447640 O2CM 8 15.9994 0.0 A 0.302905 0.502080 OR 8 15.9994 0.0 A 0.315378 0.636386 CR 6 12.0110 0.0 A 0.387541 0.230120 NC=C 7 14.0067 0.0 A 0.329632 0.836800 So its interesting for me 1- on what assumptions that blocks were generated ? 2- Why charge in [ atomtypes ] (zero) differes from the charges in the topology of the same groups? how I can check correctness of charge distribution in such itp files ? 3- What is sigma and epsilon in the [ atomtypes ] ? :) 4- Have anybody else used Swiss param for modeling protein-ligands systems? Might it be used with the charmm36 set ? 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? 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