Re: [gmx-users] charmm36 force field
On 2/12/18 3:09 PM, farial tavakoli wrote: First, please note that this line is not doing anything: define = -DUSE_OLD_C3 If you're trying to use the old CHARMM36 parameters, and not CHARMM36m, the correct keyword is -DUSE_OLD_C36. We only included that in the case that people wanted to do force field comparisons, because for folded proteins, C36 and C36m are almost identical by virtue of how we did the reparametrization. but when I checked nvt.gro by VMD , viewed the receptor and ligand went out of the box, almost completely and ligand was separated from the protein, completely. Is there anyone who can help me and advice me why it was happened? Sounds like a typical PBC imaging issue. Just use trjconv. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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 force field available for GROMACS
Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have not yet been able to add the covalent bonds necessary to reproduce the correct branched carbohydrate chains. Is there any solution for that? Roland seems to have one, although suboptimal. would it be possible to share it? Gianni -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM36-force-field-available-for-GROMACS-tp5011701p5015779.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 force field available for GROMACS
On 4/10/14, 2:51 AM, gsettanni wrote: Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have not yet been able to add the covalent bonds necessary to reproduce the correct branched carbohydrate chains. Is there any solution for that? Roland seems to have one, although suboptimal. would it be possible to share it? Using specbond.dat might help, but often these types of patches will require modification of atom types depending on the linkage, so there isn't any solution completely within pdb2gmx that will suffice, outside of building a residue from the original PRES entries in the CHARMM files, which is what it sounds like Roland's program does. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
Hi All, To follow up on a few recent issues that we have discovered and/or have been reported here, we have updated our CHARMM36 force field files. As always, they can be downloaded from: http://mackerell.umaryland.edu/CHARMM_ff_params.html Here is a list of changes: 1. An error in ions.itp was propagated from the old CHARMM27 files, which assigned a -2 charge to Zn. The .rtp entry for Zn was correct, so if you are studying any metal-containing proteins, the simulations should be fine if the topology was generated with pdb2gmx. It would only matter if you used genion to add Zn to the system, so the error would be fairly obvious in the accumulation of negative charge. 2. An atom name in the LSN (neutral lysine) .rtp entry was incorrect. This is also a rather obvious error, as pdb2gmx would die with a fatal error when trying to generate impropers. 3. Per recent posts to the list, we have corrected errors related to H5' nomenclature in RNA. Bonds would have been missing between C5' and H5'1/H5'2, causing H atoms to go flying around, or the simulation may have just simply crashed. DNA simulations done with this force field are not affected by this problem. Support for RNA has further been enhanced by the addition of .hdb entries for ADE, CYT, GUA, and URA. 4. We have added angle parameters for NH2-CT1-CT1 to fix a problem with missing angle parameters for neutral N-terminal amino acids like Ile and Thr. 5. We added heme and cholesterol (CHL1), per user requests. If anyone has comments, questions, etc. about these force field files, please feel free to post them here or send them to me. Happy simulating! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
Dear Justin, Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn bound to H2O (water) in updated CHARMM36 ff? For example, this state is important for some structures. E.g. Carbonic anhydrase. Ahmet Yıldırım 18 Mar 2014 tarihinde 18:44 saatinde, Justin Lemkul jalem...@vt.edu şunları yazdı: Hi All, To follow up on a few recent issues that we have discovered and/or have been reported here, we have updated our CHARMM36 force field files. As always, they can be downloaded from: http://mackerell.umaryland.edu/CHARMM_ff_params.html Here is a list of changes: 1. An error in ions.itp was propagated from the old CHARMM27 files, which assigned a -2 charge to Zn. The .rtp entry for Zn was correct, so if you are studying any metal-containing proteins, the simulations should be fine if the topology was generated with pdb2gmx. It would only matter if you used genion to add Zn to the system, so the error would be fairly obvious in the accumulation of negative charge. 2. An atom name in the LSN (neutral lysine) .rtp entry was incorrect. This is also a rather obvious error, as pdb2gmx would die with a fatal error when trying to generate impropers. 3. Per recent posts to the list, we have corrected errors related to H5' nomenclature in RNA. Bonds would have been missing between C5' and H5'1/H5'2, causing H atoms to go flying around, or the simulation may have just simply crashed. DNA simulations done with this force field are not affected by this problem. Support for RNA has further been enhanced by the addition of .hdb entries for ADE, CYT, GUA, and URA. 4. We have added angle parameters for NH2-CT1-CT1 to fix a problem with missing angle parameters for neutral N-terminal amino acids like Ile and Thr. 5. We added heme and cholesterol (CHL1), per user requests. If anyone has comments, questions, etc. about these force field files, please feel free to post them here or send them to me. Happy simulating! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 3/18/14, 1:32 PM, Gmail2 wrote: Dear Justin, Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn bound to H2O (water) in updated CHARMM36 ff? For example, this state is important for some structures. E.g. Carbonic anhydrase. No. We don't have any special parameters for such interactions. Sounds better suited to QM, anyway :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
Nice trick - I didn't realise you could chain and group sed regular
expressions that way!
Neither did I know pdb2gmx had an .arn database.
That's two things I've learned... Can I go home now? :-D
Mark
On Mar 10, 2014 7:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
cat $pdbfile | sed 's/TIP3/SOL /' | sed 's/ OH2 SOL/ OW SOL/' | sed 's/
H1 SOL/ HW1 SOL/' | sed 's/ H2 SOL/ HW2 SOL/' | sed 's/ SOD SOD/ NA NA
/g
' | sed 's/ CLA CLA/ CL CL /g'
Something like this in one command?:
sed 's/TIP3/SOL /;/SOL/{s/OH2/OW /;s/H1 /HW1/;s/H2 /HW2/;};s/SOD/NA
/g;s/CLA/CL /g;' $pdbfile
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
--
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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 3/9/14, 6:28 AM, jim wrote: I'm confused about the existence of H5'1 and H5'2 atom names in the RNA nucleotides (in merge.rtp). I thought all atom names followed the CHARMM 36 atom name convention. Particularly, why do atoms H2' and H2'' correspond to the latter, while H5'1 and H5'2 carry the same name as the Gromacs convention? At the same time, in [bonds] H5' and H5'' are used instead of H5'1 and H5'2. I suspect H5'1 and H5'2 should have been H5' and H5''. On the other hand, I assume H5'1 and H5'2 are correct for the DNA since there is a correspondence with H2'1 and H2'2. What we tried to do was make the fewest changes possible to CHARMM nomenclature, while still playing nice the the Gromacs .hdb and .tdb machinery. You are correct in noting the error in the [bonds] involving H5' and H5'' for RNA - I will see that this problem is fixed in our next release. Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 nomenclature. The H2' and H2'' used in RNA are correct. Since H2'' is bonded to C2' and H2' is bonded to O2', there is no issue in .hdb generation that leads to any problem, so those names were left untouched. Since, in DNA, H2' and H2'' are both bonded to C2', they needed to be renamed. Please let me know if you spot anything else that is unusual or incorrect. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
Thanks for the clarification. *Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 nomenclature.* Even though H5' and H5'' are connected to the same atom, what would be the problem to keep these H atom names H5' and H5'' instead of changing them to H5'1 and H5'2? Also, what is the significance of the -O3' P bond listed in the [bonds] of the RNA nucleotides in the previous CHARMM 27 FF? It is absent in CHARMM 36. Thanks. On Sun, Mar 9, 2014 at 6:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/9/14, 6:28 AM, jim wrote: I'm confused about the existence of H5'1 and H5'2 atom names in the RNA nucleotides (in merge.rtp). I thought all atom names followed the CHARMM 36 atom name convention. Particularly, why do atoms H2' and H2'' correspond to the latter, while H5'1 and H5'2 carry the same name as the Gromacs convention? At the same time, in [bonds] H5' and H5'' are used instead of H5'1 and H5'2. I suspect H5'1 and H5'2 should have been H5' and H5''. On the other hand, I assume H5'1 and H5'2 are correct for the DNA since there is a correspondence with H2'1 and H2'2. What we tried to do was make the fewest changes possible to CHARMM nomenclature, while still playing nice the the Gromacs .hdb and .tdb machinery. You are correct in noting the error in the [bonds] involving H5' and H5'' for RNA - I will see that this problem is fixed in our next release. Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 nomenclature. The H2' and H2'' used in RNA are correct. Since H2'' is bonded to C2' and H2' is bonded to O2', there is no issue in .hdb generation that leads to any problem, so those names were left untouched. Since, in DNA, H2' and H2'' are both bonded to C2', they needed to be renamed. Please let me know if you spot anything else that is unusual or incorrect. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] CHARMM36 force field available for GROMACS
Thanks, but I'll have to ask you something again. :) On Sun, Mar 9, 2014 at 5:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/9/14, 7:23 PM, Jim wrote: Thanks for the clarification. *Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 nomenclature.* Even though H5' and H5'' are connected to the same atom, what would be the problem to keep these H atom names H5' and H5'' instead of changing them to H5'1 and H5'2? In principle, no, the CHARMM-specific names should work fine, but only if you add corresponding entries in the merged.arn file to translate between CHARMM and Gromacs nomenclature. We made the naming change to interface smoothly with the Gromacs hydrogen-generation (.hdb) mechanism. If you have a coordinate file that complies with CHARMM naming, i.e. from CHARMM-GUI, then simple sed statements take care of any issues. Although this makes sense, it also brings other questions. I don't really understand the significance of the *hdb file - isn't its sole purpose to add hydrogens to coordinates that don't have all hydrogens? Second, what kind of a file is merged.am? I've never seen such a file... Third, if the H2' and H2'' of the RNA nucleotides do not correspond to the Gromacs nomenclature as well, then where exactly is their CHARMM-Gromacs conversion taken care of? In other words, if I use H5' and H5'' names instead of H5'1 and H5'2, isn't this equivalent to using the H2' and H2'' names instead of H2'1 and H2'2 in terms of translating between nomenclatures? Basically, I have a CHARMM 36 solvated file with all necessary hydrogens generated with CHARMM, do some rotation (for PBC matching) and then something like this: cat $pdbfile | sed 's/TIP3/SOL /' | sed 's/ OH2 SOL/ OW SOL/' | sed 's/ H1 SOL/ HW1 SOL/' | sed 's/ H2 SOL/ HW2 SOL/' | sed 's/ SOD SOD/ NA NA /g ' | sed 's/ CLA CLA/ CL CL /g' I don't change the names of any other atom or residue. I use H5' and H5''. I change ADE, GUA, CYT, URA to use the H5' and H5'' atom names in the merge.rtp as well. I don't touch the [bonds] because they already use these atom names. I generate a topology and *.gro with pdb2gmx. It looks like this (e.g. for one residue): [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 17 GUA rtp GUA q -0.5 1ON5 17GUAO5' 1 -0.6615.9994 ; qtot -0.66 2HN5 17GUAH5T 2 0.43 1.008 ; qtot -0.23 3 CN8B 17GUAC5' 3 0.05 12.011 ; qtot -0.18 4HN8 17GUAH5' 4 0.09 1.008 ; qtot -0.09 5HN8 17GUA H5'' 5 0.09 1.008 ; qtot 0 6CN7 17GUAC4' 6 0.16 12.011 ; qtot 0.16 7HN7 17GUAH4' 7 0.09 1.008 ; qtot 0.25 8 ON6B 17GUAO4' 8 -0.515.9994 ; qtot -0.25 9 CN7B 17GUAC1' 9 0.16 12.011 ; qtot -0.09 10HN7 17GUAH1' 10 0.09 1.008 ; qtot 0 11 NN2B 17GUA N9 11 -0.02 14.007 ; qtot -0.02 12CN5 17GUA C4 12 0.26 12.011 ; qtot 0.24 13NN1 17GUA N2 13 -0.68 14.007 ; qtot -0.44 14HN1 17GUAH21 14 0.32 1.008 ; qtot -0.12 15HN1 17GUAH22 15 0.35 1.008 ; qtot 0.23 16 NN3G 17GUA N3 16 -0.74 14.007 ; qtot -0.51 17CN2 17GUA C2 17 0.75 12.011 ; qtot 0.24 18 NN2G 17GUA N1 18 -0.34 14.007 ; qtot -0.1 19HN2 17GUA H1 19 0.26 1.008 ; qtot 0.16 20CN1 17GUA C6 20 0.54 12.011 ; qtot 0.7 21ON1 17GUA O6 21 -0.5115.9994 ; qtot 0.19 22 CN5G 17GUA C5 22 0 12.011 ; qtot 0.19 23NN4 17GUA N7 23 -0.6 14.007 ; qtot -0.41 24CN4 17GUA C8 24 0.25 12.011 ; qtot -0.16 25HN3 17GUA H8 25 0.16 1.008 ; qtot 0 26 CN7B 17GUAC2' 26 0.14 12.011 ; qtot 0.14 27HN7 17GUA H2'' 27 0.09 1.008 ; qtot 0.23 28ON5 17GUAO2' 28 -0.6615.9994 ; qtot -0.43 29HN5 17GUAH2' 29 0.43 1.008 ; qtot 0 30CN7 17GUAC3' 30 0.01 12.011 ; qtot 0.01 31HN7 17GUAH3' 31 0.09 1.008 ; qtot 0.1 32ON2 17GUAO3' 32
