Re: [gmx-users] zero value for non-Protein components in energygrps
Thanks Justin! That was the issue. MHK On 2017-10-31 01:35 PM, Justin Lemkul wrote: On 10/31/17 12:07 PM, Mohammad Hassan Khatami wrote: Hi, I have an issue with calculating energy groups in GMX2016.4, while running a simple protein in water tutorial using the default oplsAA forcefield in gromacs. I searched my problem it in the mailing list but did not find my answer. In addition to the default tutorial results, I wanted to print out the energy values for different components of the simulation, i.e., protein and water, in the .edr file. So I added the line below to the .mdp file to calculate values for different energy groups: energygrps = Protein SOL After running a short simulation, I calculated the different energy values and the output is as follow: Energy Average Err.Est. RMSD Tot-Drift --- LJ-14 3004.95 5.3 54.675 44.9933 (kJ/mol) Coulomb-14 7927.05 4.1 44.0138 -4.19923 (kJ/mol) LJ (SR) 21978.8 110 500.505 752.675 (kJ/mol) Coulomb (SR) -208384 220 1438.51 -1321.11 (kJ/mol) Coul-SR:Protein-Protein -208384 220 1438.51 -1321.11 (kJ/mol) LJ-SR:Protein-Protein 21978.8 110 500.505 752.675 (kJ/mol) Coul-14:Protein-Protein 7927.05 4.1 44.0138 -4.19923 (kJ/mol) LJ-14:Protein-Protein 3004.95 5.3 54.675 44.9933 (kJ/mol) Coul-SR:Protein-SOL 0 0 0 0 (kJ/mol) LJ-SR:Protein-SOL 0 0 0 0 (kJ/mol) Coul-14:Protein-SOL 0 0 0 0 (kJ/mol) LJ-14:Protein-SOL 0 0 0 0 (kJ/mol) Coul-SR:SOL-SOL 0 0 0 0 (kJ/mol) LJ-SR:SOL-SOL 0 0 0 0 (kJ/mol) Coul-14:SOL-SOL 0 0 0 0 (kJ/mol) LJ-14:SOL-SOL 0 0 0 0 (kJ/mol) Here, all the energy values for the Protein-SOL and SOL-SOL are zero, which is not what I expected. Moreover, the general LJ-14, Coulomb-14, LJ (SR) and Coulomb (SR) are exactly the values calculated for only protein. When I run them individually, i.e., only water system and only protein system, I get non-zero values, which are expected. Is there any other flag except "energygrps" that I forgot to implement in my mdp file? and why is it only calculating the values of the protein in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb (SR) energies. If you did the simulation on GPU, energygrps are not supported. Do an mdrun -rerun on the trajectory using just CPU hardware to obtain these energies. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] zero value for non-Protein components in energygrps
Hi, I have an issue with calculating energy groups in GMX2016.4, while running a simple protein in water tutorial using the default oplsAA forcefield in gromacs. I searched my problem it in the mailing list but did not find my answer. In addition to the default tutorial results, I wanted to print out the energy values for different components of the simulation, i.e., protein and water, in the .edr file. So I added the line below to the .mdp file to calculate values for different energy groups: energygrps = Protein SOL After running a short simulation, I calculated the different energy values and the output is as follow: Energy Average Err.Est. RMSD Tot-Drift --- LJ-14 3004.95 5.3 54.675 44.9933 (kJ/mol) Coulomb-14 7927.05 4.1 44.0138 -4.19923 (kJ/mol) LJ (SR) 21978.8 110 500.505 752.675 (kJ/mol) Coulomb (SR) -208384 220 1438.51 -1321.11 (kJ/mol) Coul-SR:Protein-Protein -208384 220 1438.51 -1321.11 (kJ/mol) LJ-SR:Protein-Protein 21978.8 110 500.505 752.675 (kJ/mol) Coul-14:Protein-Protein 7927.05 4.1 44.0138 -4.19923 (kJ/mol) LJ-14:Protein-Protein 3004.95 5.3 54.675 44.9933 (kJ/mol) Coul-SR:Protein-SOL 0 0 0 0 (kJ/mol) LJ-SR:Protein-SOL 0 0 0 0 (kJ/mol) Coul-14:Protein-SOL 0 0 0 0 (kJ/mol) LJ-14:Protein-SOL 0 0 0 0 (kJ/mol) Coul-SR:SOL-SOL 0 0 0 0 (kJ/mol) LJ-SR:SOL-SOL 0 0 0 0 (kJ/mol) Coul-14:SOL-SOL 0 0 0 0 (kJ/mol) LJ-14:SOL-SOL 0 0 0 0 (kJ/mol) Here, all the energy values for the Protein-SOL and SOL-SOL are zero, which is not what I expected. Moreover, the general LJ-14, Coulomb-14, LJ (SR) and Coulomb (SR) are exactly the values calculated for only protein. When I run them individually, i.e., only water system and only protein system, I get non-zero values, which are expected. Is there any other flag except "energygrps" that I forgot to implement in my mdp file? and why is it only calculating the values of the protein in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb (SR) energies. Best, MHK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CHARMM36 parameter for polysaccharide branching
Thanks Justin :) It worked. Small numbers!!! Best, MH > On May 25, 2017, at 3:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/25/17 3:00 PM, Mohammad Hassan Khatami wrote: >> Hello! >> I am trying to simulate a simple branching polysaccharide molecule. Thanks >> to you, I found and implemented the CHARMM36 parameters for the 1->4 and >> 1->6 links, however, I was not able to find the exact partial charge >> parameters for the monomer in the branching point of the polymer. In other >> words, I am looking for parameters for the monomer AAA(the name is >> arbitrary), below: >> >> 1->6 —AGM—1->4—AGF >>/ >> AGI—1->4—AAA—1->4—AGF >> >> I have combined the parameters for 1->4 (14ba) and 1->6(16ab) links from >> top_all36_carb.rtf and the simulation is running with all bonds and links >> in place, but the total charge of the system is not zero (which it should). >> My only concern is if specific parameters for the monomer in the branching >> point of the polymer, exists, and where can I find them? >> > > The same place as you got the linkages; all the PRES entries I pointed out > before (as well as the 1-6 linkages) have the correct charges and types > specified. Your charge should come out to net neutral, as the branching > doesn't impose any net charge. Check your work carefully. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CHARMM36 parameter for polysaccharide branching
Hello! I am trying to simulate a simple branching polysaccharide molecule. Thanks to you, I found and implemented the CHARMM36 parameters for the 1->4 and 1->6 links, however, I was not able to find the exact partial charge parameters for the monomer in the branching point of the polymer. In other words, I am looking for parameters for the monomer AAA(the name is arbitrary), below: 1->6 —AGM—1->4—AGF / AGI—1->4—AAA—1->4—AGF I have combined the parameters for 1->4 (14ba) and 1->6(16ab) links from top_all36_carb.rtf and the simulation is running with all bonds and links in place, but the total charge of the system is not zero (which it should). My only concern is if specific parameters for the monomer in the branching point of the polymer, exists, and where can I find them? Best, MH -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Thanks Justin! It worked. All bonds are now in place. I’ll play with the branching a bit and will make a new ticket, if I had a problem. Thank again, MH > On May 24, 2017, at 1:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/24/17 12:04 PM, Mohammad Hassan Khatami wrote: >> Sorry for that. Here are the types. >> atom type >> C1 CC3162 >> O4 OC311 > > O4 should be OC301 for all 1-4 linkages (PRES 14aa, 14ab, 14ba, 14bb in > top_all36_carb.rtf). > > -Justin > >> C4 CC3161 >> C5 CC3163 >> C3 CC3161 >> H4 HCA1 >> >> I checked them, but I was not able to find the exact combination of atoms >> angles and dihedrals associated with them in the ffbonded.itp. >> For example, I did not find C4-O4-2C1 (CC3161 OC311 CC3162) there, but I >> found both >> CC3161 CC3162OC311 >> CC3162 CC3161OC311 >> >>> On May 24, 2017, at 11:39 AM, Justin Lemkul <jalem...@vt.edu >>> <mailto:jalem...@vt.edu>> wrote: >>> >>> On 5/24/17 11:35 AM, Mohammad Hassan Khatami wrote: >>>> >>>>> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami <mhk...@mun.ca >>>>> <mailto:mhk...@mun.ca> <mailto:mhk...@mun.ca <mailto:mhk...@mun.ca>>> >>>>> wrote: >>>>> >>>>> Some how I figured out the problem and fixed it! I changed "O4 +C1" >>>>> to "O4 2C1” and it worked. I hope it is correct. >>>> Nope! the bond are not made this time! That’s why grompp did not complain! >>> >>> That's because CHARMM and GROMACS use different syntax. CHARMM patches use >>> 1 and 2 to denote the first and second residues supplied in the patch call >>> in the input script. You can't do the same thing in GROMACS. + and - are >>> to specify next and previous residue in the .rtp, respectively. pdb2gmx >>> will silently accept nonexistent atoms like 2C1 because a +/- designator >>> may exist in a terminal residue, in which case the atom won't be found. >>> >>> Your previous message is also not what I asked for. I know what the atom >>> names are, and I know what the atom types should be, but I don't know what >>> *types* you actually ended up with in the topology. Please provide the >>> *types* corresponding to the lines that generate errors. >>> >>>>> Now I have to move on to make the more complicated form of my polymer, >>>>> and add 1->6 connection to the system, like below: >>>>> >>>>> 1->6 —AGLC—1->4—AGLC. >>>>> / >>>>> AGLC—1->4—AGLC—1->4—AGLC >>>>> >>>>> Now I will rename the residues, based on their position as follow: >>>>> >>>>> 1->6 —AGM—1->4—AGF >>>>> / >>>>> AGI—1->4—AG6—1->4—AGF >>>>> >>>>> Now, I am a bit confused. This time AG6 is going to be connected to AGF >>>>> trough 1->4 bond, which I will add it to the residue using "O4 2C1” >>>>> (which I will do similar to what I did before), but for the 1->6 >>>>> connection to AGM, I would need to connect O6 of AG6 to C1 of AGM. >>>>> Should I connect it through bond O6 3C1? or O6 2C1(which would be odd!)? >>>>> >>> >>> You can do branching with specbond.dat entries (see the manual) but GROMACS >>> has difficulty with this. It is trivial to perform in CHARMM. >>> >>> -Justin >> > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu <mailto:jalem...@outerbanks.umaryland.edu> > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > <http://mackerell.umaryland.edu/~jalemkul> > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send > a mail to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Sorry for that. Here are the types. atom type C1 CC3162 O4 OC311 C4 CC3161 C5 CC3163 C3 CC3161 H4 HCA1 I checked them, but I was not able to find the exact combination of atoms angles and dihedrals associated with them in the ffbonded.itp. For example, I did not find C4-O4-2C1 (CC3161 OC311 CC3162) there, but I found both CC3161 CC3162OC311 CC3162 CC3161OC311 > On May 24, 2017, at 11:39 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > On 5/24/17 11:35 AM, Mohammad Hassan Khatami wrote: >> >>> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami <mhk...@mun.ca >>> <mailto:mhk...@mun.ca>> wrote: >>> >>> Some how I figured out the problem and fixed it! I changed "O4 +C1" to >>> "O4 2C1” and it worked. I hope it is correct. >> Nope! the bond are not made this time! That’s why grompp did not complain! > > That's because CHARMM and GROMACS use different syntax. CHARMM patches use 1 > and 2 to denote the first and second residues supplied in the patch call in > the input script. You can't do the same thing in GROMACS. + and - are to > specify next and previous residue in the .rtp, respectively. pdb2gmx will > silently accept nonexistent atoms like 2C1 because a +/- designator may exist > in a terminal residue, in which case the atom won't be found. > > Your previous message is also not what I asked for. I know what the atom > names are, and I know what the atom types should be, but I don't know what > *types* you actually ended up with in the topology. Please provide the > *types* corresponding to the lines that generate errors. > >>> Now I have to move on to make the more complicated form of my polymer, and >>> add 1->6 connection to the system, like below: >>> >>>1->6 —AGLC—1->4—AGLC. >>> / >>> AGLC—1->4—AGLC—1->4—AGLC >>> >>> Now I will rename the residues, based on their position as follow: >>> >>>1->6 —AGM—1->4—AGF >>> / >>> AGI—1->4—AG6—1->4—AGF >>> >>> Now, I am a bit confused. This time AG6 is going to be connected to AGF >>> trough 1->4 bond, which I will add it to the residue using "O4 2C1” >>> (which I will do similar to what I did before), but for the 1->6 connection >>> to AGM, I would need to connect O6 of AG6 to C1 of AGM. Should I connect >>> it through bond O6 3C1? or O6 2C1(which would be odd!)? >>> > > You can do branching with specbond.dat entries (see the manual) but GROMACS > has difficulty with this. It is trivial to perform in CHARMM. > > -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami <mhk...@mun.ca> wrote: > > Some how I figured out the problem and fixed it! I changed "O4 +C1" to > "O4 2C1” and it worked. I hope it is correct. Nope! the bond are not made this time! That’s why grompp did not complain! > Now I have to move on to make the more complicated form of my polymer, and > add 1->6 connection to the system, like below: > > 1->6 —AGLC—1->4—AGLC. > / > AGLC—1->4—AGLC—1->4—AGLC > > Now I will rename the residues, based on their position as follow: > > 1->6 —AGM—1->4—AGF > / > AGI—1->4—AG6—1->4—AGF > > Now, I am a bit confused. This time AG6 is going to be connected to AGF > trough 1->4 bond, which I will add it to the residue using "O4 2C1” (which > I will do similar to what I did before), but for the 1->6 connection to AGM, > I would need to connect O6 of AG6 to C1 of AGM. Should I connect it through > bond O6 3C1? or O6 2C1(which would be odd!)? > > > MH > >> On May 24, 2017, at 10:47 AM, Mohammad Hassan Khatami <mhk...@mun.ca> wrote: >> >> Hi Justin, >> Here are all the errors with the (atom indices) and the "atom names”. Based >> on the order of the errors I think I am making mistakes when I am trying to >> modify the AGLC units to connect them through O4-2C1 (O4 to the C1 of the >> next residue). I am some how sure that I am making mistakes in the >> connecting bond part. >> --- >> ERROR 1 [file topol.top, line 396]: (between 16 18 24)“C4-O4-2C1” —for 2C1, >> or other atoms means C1 or the other atom of the next residue. >> No default U-B types >> >> ERROR 2 [file topol.top, line 437]: (between 37 39 45)“C4-O4-2C1” >> No default U-B types >> >> ERROR 3 [file topol.top, line 549]: (between 5 16 18 24)“C5-C4-O4-2C1” >> No default Proper Dih. types >> >> ERROR 4 [file topol.top, line 550]: (between 12 16 18 24)“C3-C4-O4-2C1” >> No default Proper Dih. types >> >> ERROR 5 [file topol.top, line 551]: (between 17 16 18 24)“H4-C4-O4-2C1” >> No default Proper Dih. types >> >> ERROR 6 [file topol.top, line 552]: (between 16 18 24 25)”C4-O4-2C1-2H1” >> No default Proper Dih. types >> >> ERROR 7 [file topol.top, line 553]: (between 16 18 24 28)”C4-O4-2C1-2O5” >> No default Proper Dih. types >> >> ERROR 8 [file topol.top, line 554]: (between 16 18 24 29)”C4-O4-2C1-2C2” >> No default Proper Dih. types >> >> ERROR 9 [file topol.top, line 615]: (between 26 37 39 45)“C5-C4-O4-2C1” >> No default Proper Dih. types >> >> ERROR 10 [file topol.top, line 616]: (between 33 37 39 45)“C3-C4-O4-2C1” >> No default Proper Dih. types >> >> ERROR 11 [file topol.top, line 617]: (between 38 37 39 45)“H4-C4-O4-2C1” >> No default Proper Dih. types >> >> ERROR 12 [file topol.top, line 618]: (between 37 39 45 46)”C4-O4-2C1-2H1” >> No default Proper Dih. types >> >> ERROR 13 [file topol.top, line 619]: (between 37 39 45 49)”C4-O4-2C1-2O5” >> No default Proper Dih. types >> >> ERROR 14 [file topol.top, line 620]: (between 37 39 45 50)”C4-O4-2C1-2C2” >> No default Proper Dih. types >> --- >> >> Just as a reminder, in the first step of setting up my system, I am trying >> to make a trimer of AGLC—1->4—AGLC—1->4—AGLC. So I modified the AGLC and >> made 3 copies for the initial residue, called “AGI”, the middle one, called >> “AGM” and the final one, called “AGF”. >> I removed the unwanted atoms, modified the charges and updated the indices , >> as described in the CHARMM patch file. I also removed the bond associated >> with the atoms that I have removed. >> For both initial (AGI) and middle (AGM) ones I added the bond below in the [ >> bonds ] parts. >> O4 +C1 >> to connect the O4 to the C1 of the next residue. >> For the last one (AGF) I did not add any bonds. >> >> Thanks again, >> MH >> >>> On May 23, 2017, at 7:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>&g
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Some how I figured out the problem and fixed it! I changed "O4 +C1" to "O4 2C1” and it worked. I hope it is correct. Now I have to move on to make the more complicated form of my polymer, and add 1->6 connection to the system, like below: 1->6 —AGLC—1->4—AGLC. / AGLC—1->4—AGLC—1->4—AGLC Now I will rename the residues, based on their position as follow: 1->6 —AGM—1->4—AGF / AGI—1->4—AG6—1->4—AGF Now, I am a bit confused. This time AG6 is going to be connected to AGF trough 1->4 bond, which I will add it to the residue using "O4 2C1” (which I will do similar to what I did before), but for the 1->6 connection to AGM, I would need to connect O6 of AG6 to C1 of AGM. Should I connect it through bond O6 3C1? or O6 2C1(which would be odd!)? MH > On May 24, 2017, at 10:47 AM, Mohammad Hassan Khatami <mhk...@mun.ca> wrote: > > Hi Justin, > Here are all the errors with the (atom indices) and the "atom names”. Based > on the order of the errors I think I am making mistakes when I am trying to > modify the AGLC units to connect them through O4-2C1 (O4 to the C1 of the > next residue). I am some how sure that I am making mistakes in the > connecting bond part. > --- > ERROR 1 [file topol.top, line 396]: (between 16 18 24)“C4-O4-2C1” —for 2C1, > or other atoms means C1 or the other atom of the next residue. > No default U-B types > > ERROR 2 [file topol.top, line 437]: (between 37 39 45)“C4-O4-2C1” > No default U-B types > > ERROR 3 [file topol.top, line 549]: (between 5 16 18 24)“C5-C4-O4-2C1” > No default Proper Dih. types > > ERROR 4 [file topol.top, line 550]: (between 12 16 18 24)“C3-C4-O4-2C1” > No default Proper Dih. types > > ERROR 5 [file topol.top, line 551]: (between 17 16 18 24)“H4-C4-O4-2C1” > No default Proper Dih. types > > ERROR 6 [file topol.top, line 552]: (between 16 18 24 25)”C4-O4-2C1-2H1” > No default Proper Dih. types > > ERROR 7 [file topol.top, line 553]: (between 16 18 24 28)”C4-O4-2C1-2O5” > No default Proper Dih. types > > ERROR 8 [file topol.top, line 554]: (between 16 18 24 29)”C4-O4-2C1-2C2” > No default Proper Dih. types > > ERROR 9 [file topol.top, line 615]: (between 26 37 39 45)“C5-C4-O4-2C1” > No default Proper Dih. types > > ERROR 10 [file topol.top, line 616]: (between 33 37 39 45)“C3-C4-O4-2C1” > No default Proper Dih. types > > ERROR 11 [file topol.top, line 617]: (between 38 37 39 45)“H4-C4-O4-2C1” > No default Proper Dih. types > > ERROR 12 [file topol.top, line 618]: (between 37 39 45 46)”C4-O4-2C1-2H1” > No default Proper Dih. types > > ERROR 13 [file topol.top, line 619]: (between 37 39 45 49)”C4-O4-2C1-2O5” > No default Proper Dih. types > > ERROR 14 [file topol.top, line 620]: (between 37 39 45 50)”C4-O4-2C1-2C2” > No default Proper Dih. types > --- > > Just as a reminder, in the first step of setting up my system, I am trying to > make a trimer of AGLC—1->4—AGLC—1->4—AGLC. So I modified the AGLC and made 3 > copies for the initial residue, called “AGI”, the middle one, called “AGM” > and the final one, called “AGF”. > I removed the unwanted atoms, modified the charges and updated the indices , > as described in the CHARMM patch file. I also removed the bond associated > with the atoms that I have removed. > For both initial (AGI) and middle (AGM) ones I added the bond below in the [ > bonds ] parts. > O4 +C1 > to connect the O4 to the C1 of the next residue. > For the last one (AGF) I did not add any bonds. > > Thanks again, > MH > >> On May 23, 2017, at 7:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> >> On 5/23/17 2:16 PM, Mohammad Hassan Khatami wrote: >>> Thank Justin! >>> I finished adding the new “residues” in the .rtp file. pdb2gmx runs >>> straight forward. However, while doing energy minimizations, I get several >>> errors like the ones below, arise: >>> >>> ERROR 2 [file topol.top, line 396]: >>> No default U-B types >>> and >>> ERROR 5 [file topol.top, line 550]: >>> No default Proper Dih. types >>> >>> As it says, t
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Hi Justin, Here are all the errors with the (atom indices) and the "atom names”. Based on the order of the errors I think I am making mistakes when I am trying to modify the AGLC units to connect them through O4-2C1 (O4 to the C1 of the next residue). I am some how sure that I am making mistakes in the connecting bond part. --- ERROR 1 [file topol.top, line 396]: (between 16 18 24)“C4-O4-2C1” —for 2C1, or other atoms means C1 or the other atom of the next residue. No default U-B types ERROR 2 [file topol.top, line 437]: (between 37 39 45)“C4-O4-2C1” No default U-B types ERROR 3 [file topol.top, line 549]: (between 5 16 18 24)“C5-C4-O4-2C1” No default Proper Dih. types ERROR 4 [file topol.top, line 550]: (between 12 16 18 24)“C3-C4-O4-2C1” No default Proper Dih. types ERROR 5 [file topol.top, line 551]: (between 17 16 18 24)“H4-C4-O4-2C1” No default Proper Dih. types ERROR 6 [file topol.top, line 552]: (between 16 18 24 25)”C4-O4-2C1-2H1” No default Proper Dih. types ERROR 7 [file topol.top, line 553]: (between 16 18 24 28)”C4-O4-2C1-2O5” No default Proper Dih. types ERROR 8 [file topol.top, line 554]: (between 16 18 24 29)”C4-O4-2C1-2C2” No default Proper Dih. types ERROR 9 [file topol.top, line 615]: (between 26 37 39 45)“C5-C4-O4-2C1” No default Proper Dih. types ERROR 10 [file topol.top, line 616]: (between 33 37 39 45)“C3-C4-O4-2C1” No default Proper Dih. types ERROR 11 [file topol.top, line 617]: (between 38 37 39 45)“H4-C4-O4-2C1” No default Proper Dih. types ERROR 12 [file topol.top, line 618]: (between 37 39 45 46)”C4-O4-2C1-2H1” No default Proper Dih. types ERROR 13 [file topol.top, line 619]: (between 37 39 45 49)”C4-O4-2C1-2O5” No default Proper Dih. types ERROR 14 [file topol.top, line 620]: (between 37 39 45 50)”C4-O4-2C1-2C2” No default Proper Dih. types --- Just as a reminder, in the first step of setting up my system, I am trying to make a trimer of AGLC—1->4—AGLC—1->4—AGLC. So I modified the AGLC and made 3 copies for the initial residue, called “AGI”, the middle one, called “AGM” and the final one, called “AGF”. I removed the unwanted atoms, modified the charges and updated the indices , as described in the CHARMM patch file. I also removed the bond associated with the atoms that I have removed. For both initial (AGI) and middle (AGM) ones I added the bond below in the [ bonds ] parts. O4 +C1 to connect the O4 to the C1 of the next residue. For the last one (AGF) I did not add any bonds. Thanks again, MH > On May 23, 2017, at 7:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/23/17 2:16 PM, Mohammad Hassan Khatami wrote: >> Thank Justin! >> I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight >> forward. However, while doing energy minimizations, I get several errors >> like the ones below, arise: >> >> ERROR 2 [file topol.top, line 396]: >> No default U-B types >> and >> ERROR 5 [file topol.top, line 550]: >> No default Proper Dih. types >> >> As it says, they might be related to the angles and dihedral parameters. Do >> you have any suggestion on where (and how) to add them? > > You shouldn't need to add parameters, but without knowing what is on those > lines (more specifically, the associated atom types because the atom numbers > will mean nothing to me) there's nothing else I can say about it. The > entirety of the carbohydrate force field should already be ported over, so > missing parameters are very odd. > > -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Thank Justin! I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight forward. However, while doing energy minimizations, I get several errors like the ones below, arise: ERROR 2 [file topol.top, line 396]: No default U-B types and ERROR 5 [file topol.top, line 550]: No default Proper Dih. types As it says, they might be related to the angles and dihedral parameters. Do you have any suggestion on where (and how) to add them? Thanks again, MH >> >> On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote: >>> Hi Justin, >>> I am asked to focus on learning how to change and update the CHARMM36 >>> parameters, so I could implement the future changes and patches easier. >>> (Thus, I am not focused in the Glycan Reader, at the moment.) >>> >>> Thank you! I think I now have a better understanding of what should I do. >>> For each part of my polymer,i.e. the initial, the middle and the final >>> part, I have to modify the AGLC molecule to represent each of these parts, >>> seperately. >>> So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch >>> from the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. >>> In this case, I need to create a new version of [ AGLC ] molecule (lets >>> call it [ AGLC14 ]) in the merged.rtp, with the changes below from the the >>> top_all36_carb.rtf, applied to it: >> >> Note that your residue name must be limited to 4 characters so it can >> properly be read from the input coordinates. AGLC14 won't work. >> >>> ! equatorial-axial 1->4 linkage >>> PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4 >>> dele atom 1HO4 >>> dele atom 2HO1 >>> dele atom 2O1 >>> ATOM 1C4 CC31610.09 ! >>> ATOM 1O4 OC301-0.36 ! >>> ATOM 2C1 CC31620.29 ! >>> BOND 1O4 2C1 >>> I have to remove the HO4, HO1 and O1 lines and modify the values for the >>> C4, O4 and C1 atoms. Then, I need to add the bond of >>> >>> [ bond ] >>> … >>> O4 +C1 >>> >> >> Correct. >> >>> Then, I need to apply the bonds and angles parameters in the the >>> top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS >>> CHARMM36. >>> !IJKL R(IK) T(IKJ)PHI T(JKL) R(KL) >>> IC 1C3 1C4 1O4 2C11.5071 110.40 -86.30 121.00 1.3902 ! psi >>> IC 1C4 1O4 2C1 2O51.4560 121.00 -130.97 108.63 1.4470 ! phi >>> IC 2O5 1O4 *2C1 2C21.4470 108.63 -122.09 110.89 1.5316 >>> IC 2O5 1O4 *2C1 2H11.4470 108.63 121.92 111.32 1.0837 >>> >>> I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values >>> into the merged.vsd file, except for the PHI values. Where (and/or how) >>> should I put it? >>> Am I on the right track? >> >> You should not do this. The .vsd file is for defining virtual sites. The >> IC lines are for the CHARMM program's internal coordinate builder, >> specifying some optimized geometry (one that the force field in total should >> produce, or come very close). All the bonded parameters you need are >> already in the force field because they come from the corresponding .prm >> files. Do not adjust bonded parameter files. >> >> -Justin >> >>> >>> Thanks again for your help. >>> MH >>> >>> >>>> On May 19, 2017, at 5:36 PM, Justin Lemkul <jalem...@vt.edu >>>> <mailto:jalem...@vt.edu>> wrote: >>>> >>>> >>>> >>>> On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote: >>>>> First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf >>>>> file I found different linkages for beta-glucose, but non for >>>>> alpha-glucose. >>>>> I am trying to make a simple chain with 1->4 linkages like below: >>>>> >>>>> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose. >>>>> >>>> >>>> Linkages are not specific to the sugar; most are totally generic. A few >>>> comments suggest specific usage and may be corner cases, but your patches >>>> will be among 14aa, 14ab, 14ba, 14bb. >>>> >>>>> >>>>> Then, I might need to branch them with1->6 linkage. >>>> >>>> Also totally possible. >>>> >>>>> I tried Glycan Reader, but itstill crashes. >>>>> >>>> >>>> Uploading a correctly named PDB file should work in Glycan Reader or the >>>> Quick MD Simulator, but "still crashes" is not diagnostic of anything. >>>> Specific help with CHARMM-GUI should be brought to their attention, though. >>>> >>>> -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Hi Justin, I am asked to focus on learning how to change and update the CHARMM36 parameters, so I could implement the future changes and patches easier. (Thus, I am not focused in the Glycan Reader, at the moment.) Thank you! I think I now have a better understanding of what should I do. For each part of my polymer,i.e. the initial, the middle and the final part, I have to modify the AGLC molecule to represent each of these parts, seperately. So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to it: ! equatorial-axial 1->4 linkage PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4 dele atom 1HO4 dele atom 2HO1 dele atom 2O1 ATOM 1C4 CC31610.09 ! ATOM 1O4 OC301-0.36 ! ATOM 2C1 CC31620.29 ! BOND 1O4 2C1 I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 and C1 atoms. Then, I need to add the bond of [ bond ] … O4 +C1 Then, I need to apply the bonds and angles parameters in the the top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36. !IJKL R(IK) T(IKJ)PHI T(JKL) R(KL) IC 1C3 1C4 1O4 2C11.5071 110.40 -86.30 121.00 1.3902 ! psi IC 1C4 1O4 2C1 2O51.4560 121.00 -130.97 108.63 1.4470 ! phi IC 2O5 1O4 *2C1 2C21.4470 108.63 -122.09 110.89 1.5316 IC 2O5 1O4 *2C1 2H11.4470 108.63 121.92 111.32 1.0837 I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into the merged.vsd file, except for the PHI values. Where (and/or how) should I put it? Am I on the right track? Thanks again for your help. MH > On May 19, 2017, at 5:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote: >> First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf >> file I found different linkages for beta-glucose, but non for alpha-glucose. >> I am trying to make a simple chain with 1->4 linkages like below: >> >> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose. >> > > Linkages are not specific to the sugar; most are totally generic. A few > comments suggest specific usage and may be corner cases, but your patches > will be among 14aa, 14ab, 14ba, 14bb. > >> >> Then, I might need to branch them with1->6 linkage. > > Also totally possible. > >> I tried Glycan Reader, but itstill crashes. >> > > Uploading a correctly named PDB file should work in Glycan Reader or the > Quick MD Simulator, but "still crashes" is not diagnostic of anything. > Specific help with CHARMM-GUI should be brought to their attention, though. > > -Justin > >> MH >>> >>>> Thanks Justin. >>>> I have tried the CHARMM-GUI but it crashed. I might need to modify the >>>> order of the atoms in my PDB file, which I have created using GLYCAM-Web >>>> GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual >>>> on how to apply them (any suggestions?), so it did not go far. >>> >>> What you need to do depends on linkages. There are patches (PRES in CHARMM >>> .rtf files) that tell you how each residue is manipulated in the case of a >>> patch; refer to the CHARMM documentation online for specifics. The file >>> you'll need is top_all36_carb.rtf. >>> >>> Otherwise, use the force field files as a template to rename your input >>> structure so CHARMM-GUI can process it. This is probably the much faster >>> route. >>> >>> -Justin >>> >>>> I'll play with these two, and I'll be back. >>>> MH >>>>> On May 18, 2017, at 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>> >>>>> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote: >>>>>> Hi, >>>>>> >>>>>> I am trying to run simulations on alpha-D-glucose polymers. I have done >>>>>> these simulations using AMBER and I am wondering if it is possible to >>>>>> run them employing CHARMM36 in GROMACS, as well? >>>>>> It seams that CHARMM36 in GROMACS has only implemented monomers of >>>>>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer >>>>>> to the GROMACS? >>>>>
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose. I am trying to make a simple chain with 1->4 linkages like below: alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose. Then, I might need to branch them with1->6 linkage. I tried Glycan Reader, but it still crashes. MH > >> Thanks Justin. >> I have tried the CHARMM-GUI but it crashed. I might need to modify the order >> of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I >> have downloaded the “toppar_c36_feb16” but I did not find a manual on how to >> apply them (any suggestions?), so it did not go far. > > What you need to do depends on linkages. There are patches (PRES in CHARMM > .rtf files) that tell you how each residue is manipulated in the case of a > patch; refer to the CHARMM documentation online for specifics. The file > you'll need is top_all36_carb.rtf. > > Otherwise, use the force field files as a template to rename your input > structure so CHARMM-GUI can process it. This is probably the much faster > route. > > -Justin > >> I'll play with these two, and I'll be back. >> MH >>> On May 18, 2017, at 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote: >>>> Hi, >>>> >>>> I am trying to run simulations on alpha-D-glucose polymers. I have done >>>> these simulations using AMBER and I am wondering if it is possible to run >>>> them employing CHARMM36 in GROMACS, as well? >>>> It seams that CHARMM36 in GROMACS has only implemented monomers of >>>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer >>>> to the GROMACS? >>>> >>> >>> Sure, you can treat it like any polymer, but you'll have to create the >>> internal monomer residues yourself from the patches in the original CHARMM >>> force field files. >>> >>> Or try CHARMM-GUI; it should handle what you need and give you all the >>> necessary GROMACS inputs. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>> a mail to gmx-users-requ...@gromacs.org. >> > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu <mailto:jalem...@outerbanks.umaryland.edu> > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > <http://mackerell.umaryland.edu/~jalemkul> > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send > a mail to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Thanks Justin. I have tried the CHARMM-GUI but it crashed. I might need to modify the order of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply them (any suggestions?), so it did not go far. I'll play with these two, and I'll be back. MH > On May 18, 2017, at 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote: >> Hi, >> >> I am trying to run simulations on alpha-D-glucose polymers. I have done >> these simulations using AMBER and I am wondering if it is possible to run >> them employing CHARMM36 in GROMACS, as well? >> It seams that CHARMM36 in GROMACS has only implemented monomers of >> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to >> the GROMACS? >> > > Sure, you can treat it like any polymer, but you'll have to create the > internal monomer residues yourself from the patches in the original CHARMM > force field files. > > Or try CHARMM-GUI; it should handle what you need and give you all the > necessary GROMACS inputs. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Hi, I am trying to run simulations on alpha-D-glucose polymers. I have done these simulations using AMBER and I am wondering if it is possible to run them employing CHARMM36 in GROMACS, as well? It seams that CHARMM36 in GROMACS has only implemented monomers of alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the GROMACS? Best, Mohammad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
