Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem
On 9/2/13 2:02 PM, Golshan Hejazi wrote: Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right: title= geometry-optimization cpp = /usr/bin/cpp include = integrator = steep comm_mode= Linear dt = 0.001 nsteps = 100 ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 10 xtc_grps = System energygrps = System pbc = xyz nstlist = 10 epsilon_r= 1. ns_type = grid ; or grid I don't know coulombtype = pme vdwtype = Cut-off fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = yes rlist= 0.8 rcoulomb = 0.8 rvdw = 0.8 emtol= 1.0 Note that your cutoffs are incorrect for strict adherence to CHARMM settings. See extensive threads from recent days and weeks on this topic. Yes, I am dealing with single molecule of ethanol. I can attach the tpr file and the resulting trr and gro file but it seems that the file size is big. The mailing list does not accept attachments, nor are those files particularly informative (maybe the .gro, but that can easily just be pasted in an email for a single-molecule system). Screenshots linked from some publicly accessible image-sharing site work well. When I visualize the trajectory. in the second step, the molecule is already without any bond ... it is separated atoms. I don't think this is visualization problem since I already tried all trjconv -pbc option. Measurements of intramolecular distances are more informative than whether or not visualization software thinks there's actually a bond there. The topology is definitive, visualization is not. There may certainly be a problem, but be sure you're using quantitative assessments, not qualitative (and error-prone). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem
Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right: title = geometry-optimization cpp = /usr/bin/cpp include = integrator = steep comm_mode = Linear dt = 0.001 nsteps = 100 ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc-precision = 10 xtc_grps = System energygrps = System pbc = xyz nstlist = 10 epsilon_r = 1. ns_type = grid ; or grid I don't know coulombtype = pme vdwtype = Cut-off fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = yes rlist = 0.8 rcoulomb = 0.8 rvdw = 0.8 emtol = 1.0 Yes, I am dealing with single molecule of ethanol. I can attach the tpr file and the resulting trr and gro file but it seems that the file size is big. When I visualize the trajectory. in the second step, the molecule is already without any bond ... it is separated atoms. I don't think this is visualization problem since I already tried all trjconv -pbc option. I am very confused. Thank for helping G. From: Justin Lemkul To: Discussion list for GROMACS users Sent: Monday, September 2, 2013 1:34 PM Subject: Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem Please make sure to keep the discussion on the mailing list. On 9/2/13 1:27 PM, Golshan Hejazi wrote: > This is the gro file that I am using: > ETHANOL > 9 > 1ETHA C1 1 3.133 3.266 0.008 > 1ETHA O1 2 3.244 3.350 -0.021 > 1ETHA HO1 3 3.324 3.296 -0.015 > 1ETHA H11 4 3.143 3.225 0.111 > 1ETHA H12 5 3.129 3.182 -0.065 > 1ETHA C2 6 3.007 3.351 -0.002 > 1ETHA H21 7 3.011 3.435 0.071 > 1ETHA H22 8 2.998 3.394 -0.104 > 1ETHA H23 9 2.917 3.290 0.019 > 3.41840 3.44350 3.38360 > > This is what I added in the rtp: > > [ ETHA ] > [ atoms ] > C1 CG321 0.05 0 > O1 OG311 -0.65 1 > HO1 HGP1 0.42 2 > H11 HGA2 0.09 3 > H12 HGA2 0.09 4 > C2 CG331 -0.27 5 > H21 HGA3 0.09 6 > H22 HGA3 0.09 7 > H23 HGA3 0.09 8 > [ bonds ] > C1 C2 > C1 O1 > C1 H11 > C1 H12 > O1 HO1 > C2 H21 > C2 H22 > C2 H23 > > And this is the resulting topology: > > ; Include forcefield parameters > #include "./charmm36.ff/forcefield.itp" > > [ moleculetype ] > ; Name nrexcl > drug 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > ; residue 1 ETHA rtp ETHA q 0.0 > 1 CG321 1 ETHA C1 1 0.05 12.011 ; qtot >0.05 > 2 OG311 1 ETHA O1 2 -0.65 15.9994 ; qtot >-0.6 > 3 HGP1 1 ETHA HO1 3 0.42 1.008 ; qtot >-0.18 > 4 HGA2 1 ETHA H11 4 0.09 1.008 ; qtot >-0.09 > 5 HGA2 1 ETHA H12 5 0.09 1.008 ; qtot >0 > 6 CG331 1 ETHA C2 6 -0.27 12.011 ; qtot >-0.27 > 7 HGA3 1 ETHA H21 7 0.09 1.008 ; qtot >-0.18 > 8 HGA3 1 ETHA H22 8 0.09 1.008 ; qtot >-0.09 > 9 HGA3 1 ETHA H23 9 0.09 1.008 ; qtot >0 > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 > 1 4 1 > 1 5 1 > 1 6 1 > 2 3 1 > 6 7 1 > 6 8 1 > 6 9 1 > > [ pairs ] > ; ai aj funct c0 c1 c2 c3 > 2 7 1 > 2 8 1 > 2 9 1 > 3 4 1 > 3 5 1 > 3
Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem
Please make sure to keep the discussion on the mailing list. On 9/2/13 1:27 PM, Golshan Hejazi wrote: This is the gro file that I am using: ETHANOL 9 1ETHAC11 3.133 3.266 0.008 1ETHAO12 3.244 3.350 -0.021 1ETHA HO13 3.324 3.296 -0.015 1ETHA H114 3.143 3.225 0.111 1ETHA H125 3.129 3.182 -0.065 1ETHAC26 3.007 3.351 -0.002 1ETHA H217 3.011 3.435 0.071 1ETHA H228 2.998 3.394 -0.104 1ETHA H239 2.917 3.290 0.019 3.41840 3.44350 3.38360 This is what I added in the rtp: [ ETHA ] [ atoms ] C1 CG321 0.050 O1 OG311 -0.65 1 HO1 HGP10.422 H11 HGA20.093 H12 HGA20.094 C2 CG331 -0.27 5 H21 HGA30.096 H22 HGA30.097 H23 HGA30.098 [ bonds ] C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 C2 H21 C2 H22 C2 H23 And this is the resulting topology: ; Include forcefield parameters #include "./charmm36.ff/forcefield.itp" [ moleculetype ] ; Namenrexcl drug3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 ETHA rtp ETHA q 0.0 1 CG321 1 ETHA C1 1 0.05 12.011 ; qtot 0.05 2 OG311 1 ETHA O1 2 -0.6515.9994 ; qtot -0.6 3 HGP1 1 ETHAHO1 3 0.42 1.008 ; qtot -0.18 4 HGA2 1 ETHAH11 4 0.09 1.008 ; qtot -0.09 5 HGA2 1 ETHAH12 5 0.09 1.008 ; qtot 0 6 CG331 1 ETHA C2 6 -0.27 12.011 ; qtot -0.27 7 HGA3 1 ETHAH21 7 0.09 1.008 ; qtot -0.18 8 HGA3 1 ETHAH22 8 0.09 1.008 ; qtot -0.09 9 HGA3 1 ETHAH23 9 0.09 1.008 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 4 1 1 5 1 1 6 1 2 3 1 6 7 1 6 8 1 6 9 1 [ pairs ] ; aiaj functc0c1c2c3 2 7 1 2 8 1 2 9 1 3 4 1 3 5 1 3 6 1 4 7 1 4 8 1 4 9 1 5 7 1 5 8 1 5 9 1 [ angles ] ; aiajak functc0c1c2c3 2 1 4 5 2 1 5 5 2 1 6 5 4 1 5 5 4 1 6 5 5 1 6 5 1 2 3 5 1 6 7 5 1 6 8 5 1 6 9 5 7 6 8 5 7 6 9 5 8 6 9 5 [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 4 1 2 3 9 5 1 2 3 9 6 1 2 3 9 2 1 6 7 9 2 1 6 8 9 2 1 6 9 9 4 1 6 7 9 4 1 6 8 9 4 1 6 9 9 5 1 6 7 9 5 1 6 8 9 5 1 6 9 9 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name ETHANOL [ molecules ] ; Compound#mols drug1 All of this looks perfectly normal. What are you trying to do when it flies apart? Are you dealing with a single molecule only? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem
On 9/2/13 12:59 PM, Golshan Hejazi wrote: Hello, I am trying to add ethanol as a new residue to CGenFF force field in gromacs. Basically, I need to bring this information from charmm rtf file to the gromacs format. This is the information taken from rtf file of charmm. RESI ETOH 0.00 ! C2H6O Ethanol, adm jr. GROUP ATOM C1 CG3210.05 ! H21 H11 H12 ATOM O1 OG311 -0.65 ! \ \ / ATOM HO1 HGP1 0.42 ! H22--C2--C1 ATOM H11 HGA2 0.09 ! / \ ATOM H12 HGA2 0.09 ! H23O1--HO1 GROUP ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 BOND C2 H21 C2 H22 C2 H23 DONO HO1 O1 ACCE O1 ! for ic build IC O1 C1 C2 H21 0. 0. 180. 0. 0. IC C1 H21 *C2 H22 0. 0. 120. 0. 0. IC C1 H21 *C2 H23 0. 0. 240. 0. 0. IC O1 C2 *C1 H11 0. 0. 240. 0. 0. IC O1 C2 *C1 H12 0. 0. 120. 0. 0. IC C2 C1 O1 HO1 0. 0. 180. 0. 0. I have added The ATOM and BOND information to the aminoacid.rtp file. I thought that the rest of the information are optional and pdb2gmx doesn't complain while generating the topology. But when I use the topology and gro file to do a minimization. The molecule bonds break apart and what I see is an exploded molecule. Please post your complete .rtp entry and the contents of the resulting .top file. So I thought probably the rest of the information are important too, for example: DONO HO1 O1 ACCE O1 But I dont know where to put them. These lines are only used by CHARMM during hydrogen bond analysis or in the archaic form that included a hydrogen bonding term to the energy function. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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] adding ETHANOL to CGennFF in gromacs has problem
Hello, I am trying to add ethanol as a new residue to CGenFF force field in gromacs. Basically, I need to bring this information from charmm rtf file to the gromacs format. This is the information taken from rtf file of charmm. RESI ETOH 0.00 ! C2H6O Ethanol, adm jr. GROUP ATOM C1 CG321 0.05 ! H21 H11 H12 ATOM O1 OG311 -0.65 ! \ \ / ATOM HO1 HGP1 0.42 ! H22--C2--C1 ATOM H11 HGA2 0.09 ! / \ ATOM H12 HGA2 0.09 ! H23 O1--HO1 GROUP ATOM C2 CG331 -0.27 ATOM H21 HGA3 0.09 ATOM H22 HGA3 0.09 ATOM H23 HGA3 0.09 BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1 BOND C2 H21 C2 H22 C2 H23 DONO HO1 O1 ACCE O1 ! for ic build IC O1 C1 C2 H21 0. 0. 180. 0. 0. IC C1 H21 *C2 H22 0. 0. 120. 0. 0. IC C1 H21 *C2 H23 0. 0. 240. 0. 0. IC O1 C2 *C1 H11 0. 0. 240. 0. 0. IC O1 C2 *C1 H12 0. 0. 120. 0. 0. IC C2 C1 O1 HO1 0. 0. 180. 0. 0. I have added The ATOM and BOND information to the aminoacid.rtp file. I thought that the rest of the information are optional and pdb2gmx doesn't complain while generating the topology. But when I use the topology and gro file to do a minimization. The molecule bonds break apart and what I see is an exploded molecule. So I thought probably the rest of the information are important too, for example: DONO HO1 O1 ACCE O1 But I dont know where to put them. Thanks G. -- gmx-users mailing listgmx-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
