[gmx-users] Re: Question : Ion distribution around Cl fix
Hi, I do not understand the question. Specify what force field you used, what parameters, what is Cl fix etc. etc and please send it back to the gmx-users mailing list: gmx-users@gromacs.org Regards, Pär 6 jul 2011 kl. 15.59 skrev s_akbarshahi: > > > > Hello Mr bjelkmar > I wanted to ask which graphs the density of sodium is correct ? > > Box : 2.65 *2.65 *2.65 nm > > Na : 10 > > Cl : 9 > > Cl fix : 1 > > Time : 4 ns > > Water : TIP3P > > Kind Regard > > saeed.akbarshahi > > Msc soft matter in university of guilan > --- End of Forwarded Message --- > > -- > Open WebMail Project (http://openwebmail.org) > --- End of Forwarded Message --- > > -- > Open WebMail Project (http://openwebmail.org) > --- End of Forwarded Message --- > > -- > Open WebMail Project (http://openwebmail.org) > --- End of Forwarded Message --- > > > -- > Open WebMail Project (http://openwebmail.org) > -- 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] Re: adding ff parameter of modified residue to charmm ff
T1 HB 0.105 3 180.00 ! >> NR2C CP2C CT1 NH10.105 3 180.00 ! >> NR2C CP2C CT1 CT20.105 3 180.00 ! >> NR1C CP2C CT1 HB 0.105 3 0.00 ! >> >> >> IMPROPER >> ! >> !V(improper) = Kpsi(psi - psi0)**2 >> ! >> !Kpsi: kcal/mole/rad**2 >> !psi0: degrees >> !note that the second column of numbers (0) is ignored >> ! >> !atom types Kpsi psi0 >> ! >> CP2C NR2C NR1C CT1 0.5 0 0.00 >> CP2C NR1C NR2C CT1 0.5 0 0.00 >> ! >> CP1C NR1C CP1C OCH 0.5 0 0.00 >> CP1C CP1C NR1C OCH 0.5 0 0.00 >> ! >> NR1C CP1C CP2C CT2 0.45 0 0.00 >> NR1C CP2C CP1C CT2 0.45 0 0.00 >> ! >> CP1C NR2C CP1C CE1C 220.0 0 0.00 >> CP1C CP1C NR2C CE1C 220.0 0 0.00 >> >> >> ! >> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] >> ! >> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) >> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j >> ! >> !atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 >> ! >> !CAc5.00 -0.07 1.992400 ! ALLOW ARO >> !! benzene (JES) >> CA15.00 -0.07 1.992400 ! ALLOW ARO >> CA25.00 -0.07 1.992400 ! ALLOW ARO >> CA35.00 -0.07 1.992400 ! ALLOW ARO >> CA45.00 -0.07 1.992400 ! ALLOW ARO >> CE1c 0.00 -0.068000 2.09 ! >> ! for propene, yin/adm jr., 12/95 >> CP1c 0.00 -0.05 1.80 ! ALLOW ARO >>! adm jr., 10/23/91, imidazole solvation and sublimation >> CP2c 0.00 -0.05 1.80 ! ALLOW ARO >>! adm jr., 10/23/91, imidazole solvation and sublimation >> CT3c 0.00 -0.08 2.06 0.00 -0.01 1.90 >> ! ALLOW ALI >>! methane/ethane a.i. and ethane pure solvent, adm jr, >> 2/3/92 >> ! >> Hch -2.00 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC >>! same as TIP3P hydrogen, adm jr., 7/20/89 >> HAc0.00 -0.022000 1.32 ! ALLOW PEP ALI POL SUL ARO PRO ALC >>! methane/ethane a.i. and ethane pure solvent, adm jr, >> 2/3/92 >> HA1c 0.00 -0.031000 1.25 ! >>! for propene, yin/adm jr., 12/95 >> HPc0.00 -0.03 1.358200 0.00 -0.03 1.358200 >> ! ALLOW ARO >>! JES 8/25/89 values from Jorgensen fit to hydration energy >> ! >> NR1c 0.00 -0.20 1.85 ! ALLOW ARO >>! His, adm jr., 9/4/89 >> NR2c 0.00 -0.20 1.85 ! ALLOW ARO >>! His, adm jr., 9/4/89 >> ! >> !Och0.00 -0.12 1.70 0.00 -0.12 1.40 >> ! ALLOW PEP POL >> !! This 1,4 vdW allows the C5 dipeptide minimum to >> exist.(LK) >> Och0.00 -0.12 1.70! ALLOW PEP POL, suppression du >> terme 1,4 (N.R. 10/2000) >> OHc0.00 -0.152100 1.77 ! ALLOW ALC ARO >>! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) >> >> HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use >> ! READ PARAM APPEND CARD >> ! to append hbond parameters from the file: par_hbond.inp >> >> END >> >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com <><><><><><><><><><><><><><><><><><><><><> Pär Bjelkmar, Ph.D. student Stockholm Center for Biomembrane Research (CBR), Stockholm Bioinformatics Center (SBC), Department of Biochemistry and Biophysics (DBB), Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><><><><> -- 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] Re: CMAP error
Hi, this residue must have been missed. I fixed this in 4.5 branch. /Pär Vidarebefordrat brev: > Dear Justin, > > Thanks for your advice. You were wright. The problem was solved adding > the new residue name to residuetypes.dat > > The issue was that when pdb2gmx found an unknown residue name, it > defined as "Others" system instead of "Protein". As a consequence, > the chain was capped there, adding a COO- termination to the "last" > residue of the protein. > > Thanks again for the fast and efficient answer. > > Jon -- 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] Re: HEME Charmm Force field in Gromacs format
Hi, You should install the 4.5.3 version of GROMACS which has support for heme (see gromacs homepage). Regards, Pär Bjelkmar 27 nov 2010 kl. 06.12 skrev shahid nayeem: > Hi > I am need of charmm27 forcefield in gromacs form. I am trying to simulate > heme protein which is bonded to MET S and HIS N. Please help me. I downloaded > the files from site but these do not have topology of heme. waiting for your > response. > Shahid Nayeem > Ph. D student > IIT Delhi > India <><><><><><><><><><><><><><><><><><><><><> Pär Bjelkmar, Ph.D. student Stockholm Center for Biomembrane Research (CBR), Stockholm Bioinformatics Center (SBC), Department of Biochemistry and Biophysics (DBB), Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><><><><> -- 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] Re: Can I have the mdp file?
Hi, I forward this discussion to the mailing list now because I think that it might be of interest to some people at least. Please find the mdp file of the GROMACS runs attached. To get the energies between GROMACS and CHARMM to match one has to do at least two things: * make sure the molecular conformation is _exactly_ the same. I.e. the coordinates of the atoms should be identical (inclusive correct number of significant figures) * run without cut-offs Regards, Pär Bjelkmar md.mdp Description: Binary data 17 nov 2010 kl. 13.16 skrev Xin Chen: > yes, I have done. But the potential calculated by these two methods differs > greatly. And the difference between the two is more than 10kj/mol. The CHARMM > calculation seems fine. > I guess that I set the parameters wrong in the mdp file during the GROMACS > calculation... > > > > >> -----Original E-mail- >> From: "Pär Bjelkmar" >> Sent Time: 2010-11-17 16:18:18 >> To: "Xin Chen" >> Cc: >> Subject: Re: Can I have the mdp file? >> >> Hi, >> >> I do not fully understand what you're trying to do. To reproduce Table 1 you >> need to run the program CHARMM as well as GROMACS, have you already done >> that? >> >> /Pär >> >> 17 nov 2010 kl. 03.24 skrev Xin Chen: >> >>> >>> Professor Bjelkmar: >>> hello, I've finished the article that you referred to me in your last >>> mail. It's quite helpful and thank you. But I have some trouble when I test >>> some amoni acid. The results couldn't get well with the table1 in the >>> article. I considered whether I caculated in the same way as you did, >>> especially the mdp options for Gromacs. >>> So, can I have the mdp file when you make the table? The table is also >>> sent as an attachment. >>> Thank you and Best Wishes! >>> Xin Chen >>> 2010.11.17 >>> >> > -- 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] Re: the charmm force field in gromacs
Hello, I forward your e-mail to the gmx-users mailing list so that other can see and get help from this. I don't fully understand your question but the testing went as this: We took small peptides (tripeptides typically) of arbitrary conformations of the amino acids and compared the energies of that particular configuration between the force field (CHARMM in this case) in GROMACS and in the CHARMM _program_. If they match, it of course means that the functional forms and parameters are correctly converted to GROMACS. For more information take a look in Bjelkmar et al. JCTC 2010. Please post to this list for future correspondance. Regards, Pär Bjelkmar 10 nov 2010 kl. 15.29 skrev Xin Chen: > > Professor Bjelkmar: >Hello, I am a student studying for molecular simulation. When comparing > parameter files for different force fields, I met some difficulties. As > you've said you have tested version 1.0 on all aminoacids (in addition to > lignin and cellulose), I mail this to find whether i could get some help. > Could you tell me the conformations of these aminoacids and the steps for > testing. Thank you very much. Best wishes. > Xin Chen > 2010.11.10 > > -- 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] Single atom charge group implementation for CHARMM27 in 4.5.2
Hi, all this has now been fixed I hope. The residues that I had missed are the ones my scripts not directly parse from the CHARMM ff files, i.e. they are hardcoded and hence I forgot to update the charge groups on them. Berk has now added an option of -1 to atoms added to terminals so that they become single charge groups as well, so that should be fine also. Let me know if I forgot something. Regards, Pär Bjelkmar > Message: 2 > Date: Wed, 3 Nov 2010 20:10:08 + > From: Thomas Piggot > Subject: Re: [gmx-users] Single atom charge group implementation for > CHARMM27in 4.5.2 > To: Discussion list for GROMACS users > Message-ID: <4cd1c1a0.4060...@soton.ac.uk> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Berk, > > Thanks for the information, I just wanted to make sure that my message > had not been missed. > > Cheers > > Tom > > On 03/11/10 19:37, Berk Hess wrote: >> I forgot to say that for the water models the rtp entries are only >> used to recognize >> the atoms. For the topology the itp files in the .ff dir are used. >> >> Berk >> >> >> From: g...@hotmail.com >> To: gmx-users@gromacs.org >> Subject: RE: [gmx-users] Single atom charge group implementation for >> CHARMM27 in 4.5.2 >> Date: Wed, 3 Nov 2010 20:32:58 +0100 >> >> Hi, >> >> I saw your message, but I wanted to discuss with others before answering. >> I have not had a chance for that yet, but I can answer anyhow. >> >> 1. This is a mistake. The person converting the original Charmm files >> edited his conversion >> script, but the "special cases" can not be treated with this script. >> We'll update them. >> >> 2. Water is always a special case. It charge group is smaller than >> most other charge >> groups and force field independent. For performance reasons we don't >> want to change this. >> (although in a future release we might get rid of the complete charge >> group concept) >> >> 3. Termini charge groups were also overlooked. We can fix this. I >> added support >> for charge group numbers in the tdb file some time ago. >> >> Berk >> >>> Date: Wed, 3 Nov 2010 14:50:34 + >>> From: t.pig...@soton.ac.uk >>> To: gmx-users@gromacs.org >>> Subject: [gmx-users] Single atom charge group implementation for >> CHARMM27 in 4.5.2 >>> >>> Hi, >>> >>> I sent this message a few days ago to the list but have not had a >> reply. >>> I feel some of the issues are quite important and so I am sending it >> again: >>> >>> >>> I have a few questions/comments about the implementation of the single >>> atom charge groups with the CHARMM27 force field that maybe someone can >>> help with: >>> >>> 1. There are some entries in aminoacids.rtp which have not been >>> converted to having every atom in a separate charge group (ASPP, CYS2, >>> GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I >>> understand these are some of the less commonly used entries, have they >>> been left out for a reason? By the way I also noticed during a quick >>> test for this that there is not an rtp entry for ARGN but it is given as >>> an option by pdb2gmx when using -inter. >>> >>> 2. Relating to 1 are the charge groups in the water models, which have >>> also been left as a water in a single charge group. I think I remember >>> reading somewhere that this is needed for the fast water loops in >>> GROMACS, so I assume this has been done on purpose. My concern is that >>> this is different to the TIP3P and TP3M entries in the aminoacids.rtp >>> file. If this has been done on purpose for the water models, then maybe >>> TIP3 and TP3M should also just have one charge group (as in the HOH >> entry)? >>> >>> 3. Finally, another concern I have is that when adding termini to a >>> protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal >>> atoms are still added as one charge group by pdb2gmx. I am not sure of a >>> way around this, apart from still using the -nochargegrp option, or >>> having AMBER forcefield style rtp entries for the N and C terminal >>> residues (undesirable I am sure). >>> >>> Cheers >>> >>> Tom >>> >>> On 30/10/10 20:56, Rossen Apostolov wrote: >>>> Dear Gromacs users a
[gmx-users] Re: CT3 terminal
Hello, > I use pdb2gmx command to convert a pdb file to a .gro and .top file(using > CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3. > When I use editconf to get a pdbfile from the .gro file generated, the C=0 > and the NCH3 seem to clash in space in pymol. > > Is there a way of correcting this? this sounds fishy, might be an error in the formation of the CT3. Have to look into that. What GROMACS version are you running? /Pär Bjelkmar-- 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] CHARMM36 lipid bilayers
I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär > Hi Sven, > > Yes I have tested values of rvdw-switch and (unlike in your test) have > seen a large impact of the area per lipid. Indeed this can also be seen > in the Klauda paper where they show a decreased area per lipid (~63 A^2 > to ~58 A^2) in the NAMD DPPC simulations (see the graph in the > Supporting Info) using a 1.1 nm cut-off for the switching compared to > the 0.8 nm cut-off in their CHARMM simulations. > > I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM > tip3p water. This gives me the closest results in terms of area per > lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM > results) and experiment. > > Cheers > > Tom > > Sven Jakobtorweihen wrote: >> Hi there, >> >> Tom, thanks for this hint, yes, that is an improvement. I am looking >> forward to your paper. Berk, I am using switch for vdw. Although for my >> taste switching from 0.8 to 1.2 was quite large, I used it because the >> charmm paper used these values. But I just realized that the >> implementation of the switch is different in gromacs and charmm, I >> should have seen that earlier. I think I will increase rvdw_switch to >> 1.0. However, a couple of days ago I tested already the influence of the >> switching region and it wasn't dramatic, at least for the test case. >> Nevertheless, matching the settings used in the parametrization is >> always advisable. Tom, do you have tested any cutoff settings? >> >> Cheers, >> Sven >> >> Berk Hess schrieb: >>> Hi, >>> >>> Another comment on your interaction settings. >>> You did not mail if you are using shift or switch for vdw. >>> But I guess that both probably don't match exactly what Charmm does. >>> Since the switching range is so long and this is where a large part >>> of the dispersion attraction acts, this might have a large effect on >>> the area. >>> >>> Berk >>> >>>> Date: Thu, 21 Oct 2010 16:47:21 +0100 >>>> From: t.pig...@soton.ac.uk >>>> To: gmx-users@gromacs.org >>>> Subject: Re: [gmx-users] CHARMM36 lipid bilayers >>>> >>>> Hi Sven, >>>> >>>> I have also seen similar things from the area per lipid of the bilayers >>>> I have run (POPC and DPPC). I would suggest you try running with the >>>> CHARMM TIP3P water (tips3p.itp) and see if you get values which are >>>> closer to the ones published in the paper you mention. This will be >>>> discussed in a paper which we hope to have published fairly soon. >>>> >>>> Cheers >>>> >>>> Tom >>>> >>>> Sven Jakobtorweihen wrote: >>>>> Dear gmx-users, >>>>> >>>>> recently Pär Bjelkmar and Thomas Piggot have generated force field >>> files >>>>> for Charmm36 lipids. I run some simulations to find the best run >>>>> parameters and to check if the results of the original Charmm36 lipid >>>>> article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be >>>>> reproduced with gromacs. >>>>> >>>>> I run 40 ns NPT simulations with semiisotropic pressure coupling >>>>> (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and >>>>> averages were calculated for the last 30 ns. DMPC and POPC at 303 >>> K and >>>>> DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with >>>>> pdb2gmx -nochargegrp. All simulations contained 128 lipids and >>>>> approximately the same water/lipid ratio (water is TIP3P) as Klauda et >>>>> al. I started from charmm27 bilayers provided at the Chramm Gui >>> website. >>>>> I used the following parameters: >>>>> >>>>> rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; >>>>> rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; >>>>> nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 >>>>> >>>>> These simulations result in the following area per lipid [A^2/lipid]: >>>>> DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 >>>>> >>>>> Comparing to the results of Klauda et al (all simulation with the >>>>> charmm-package, except one): >>>>> DM
Re: [gmx-users] charmm c36 lipids
> Date: Fri, 1 Oct 2010 16:27:29 +0100 > From: Thomas Piggot > Subject: Re: [gmx-users] charmm c36 lipids > To: Discussion list for GROMACS users > Message-ID: <4ca5fde1.8050...@soton.ac.uk> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > For a POPC bilayer then both your and my files produce the same tpr's > (checked both with gmxcheck and gmxdump). This is pleasing as I not only > scripted the conversions but did some parts by hand! I shall check the > other lipids to make sure that there are no discrepancies in these. Good! > > Also for my files I have included the bonded and non-bonded parameters > with parameters from CHARMM27 so as to allow simulations in water and > with proteins. I want to re-check these before contributing the > forcefield to the website, so it will probably be next week before I > upload it. Just to let you know I will use your lipids.rtp as it has the > atoms in separate charge groups so as to avoid having to use > -nochargegrp with pdb2gmx, whilst mine doesn't. I hope this is fine with > you. For sure it is but you should be aware (and I think you are, since you were involved in the September discussion about this) that GROMACS does not treat charge groups as CHARMM does. See messages with subject "ARG Charmm gmx 4.5.1" (seems like the gmx-mailing list db is down so cannot provide you with a direct link). /Pär -- 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] charmm c36 lipids
Hi Tom, great do that! If there're no discrepancies and you have tested it we should probably put your version among the user contributions. Let me know how it goes! /Pär > Hi Par, > > I have a working version of the CHARMM36 lipids that I converted myself, > which I am fairly confident is correct. I shall check your parameters > against my ones to confirm everything is the same and report back to the > list. I don't see anything which would not work for your script as there > are not any major changes to the forcefield in CHARMM36. -- 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] charmm c36 lipids
Hello Sven, Drew and gmx-users, I've gotten requests from users that want to use the c36 CHARMM lipids in GROMACS (see below). So I answer both of you and the rest of the community in this e-mail. I have a script that parses the top and par files of CHARMM force field(s). It's not the most general piece of code there is so it will not be able to convert files that do not follow the format the CHARMM top and par files had when I wrote it (version c32b1). Also, it cannot parse the toppar files (i.e. what's called the toppar stream files in CHARMM). I downloaded the force field from: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz My script is able to parse the top_lipid_all36.rtf and par_all36_lipid.prm files without any errors and generate the corresponding GROMACS rtp, atp, bonded and nonbonded files. I'm not an CHARMM expert but if they haven't changed the force field considerable lately (by changing parameter definitions and functional forms of the force field for example) the files generated by the script should be the correct GROMACS translation. However, I cannot guarantee that all went well so I would suggest that those of you who are interested in this look through the files and convince yourself that the script did the job before running production runs with these parameters. I've put it on the old (and outdated) port homepage (http://www.dbb.su.se/User:Bjelkmar/Ffcharmm) so that those of you who are interested in this can access and test it. If nothing seems to be wrong after some of you have tested it I'm going to add it to the user contributions on gromacs.org. Regards, Pär Bjelkmar 1 okt 2010 kl. 09.53 skrev Sven Jakobtorweihen: > Dear Pär Bjelkmar, > > thanks for implementing the CHARMM force field into GROMACS, that is really > useful. Recently the CHARMM developers have introduced an updated lipid force > field CHARMM36 for lipids, see Klauda et al. J. Phys. Chem. B, 2010, 114, > 7830 (doi: 10.1021/jp101759q). It seems that this is an important improvement > over the preceding version. I checked gromacs version 4.5.1 and the > git-repository; unfortunately, the charmm36 lipids are not yet available in > gromacs. However, I could write some scripts to convert the charmm files to > gromacs files, I have the feeling the bonded parameter conversion is straight > forward (having the charmm27 files for gromacs), but I fear that transferring > the bonded parameters is tedious. So my question is: Do you have by any > change already gromacs files for charmm36 lipids? Or are scripts available to > convert charmm FF to gromacs FF files? I am aware of the charmm_to_gromacs > perl scripts on the gromacs website. But as fare as I know they are not > compatible with the official implementation of charmm in gromacs, or am I > wrong? > > Thanks for your help. > > Best regards, > Sven > > -- > * > Dr.-Ing. Sven Jakobtorweihen > > Hamburg University of Technology > Institute of Chemical Reaction Engineering / V2 > Eissendorfer Str. 38 > 21073 Hamburg > Germany > > PHONE : ++49 (0) 40 42878 2491 > FAX : ++49 (0) 40 42878 2145 > E-MAIL: jakobtorwei...@tuhh.de > * > > 3 sep 2010 kl. 20.56 skrev Drew Bennett: > >> Dear Pr Bjelkmar, >> >> I saw on the gromacs mailing list that you have python a script for >> converting CHARMM ff to GMX. >> I would greatly appreciate if you could please send it to me. >> I am trying to use the new CHARMM36 lipids for a simulation with a membrane >> protein. >> >> Thank-you. >> Drew Bennett > -- 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] CHARMM lipids
Hi Yuanyuan, I send a copy of this discussion to gmx-users. We can continue the discussion there so other users can benefit from it. 27 aug 2010 kl. 09.27 skrev yuanyuan3201003: > Dear professor, > Thanks for your reply , but the lipid parameter in gromacs 4.5 beta2 is not > including DPPC,DPPS ,DPPG , is there any method that I can get the parameter > file ? Ok - it's one of those lipids you're interested in. Actually, we discussed this in gmx-developersa few days ago: http://lists.gromacs.org/pipermail/gmx-developers/2010-August/004643.html So, the conclusion is that there might be a way to include these residues as they are described in CHARMM (by building them from "patches") but that requires code changes in GROMACS in the line of what Roland suggests. This might or might not happen. If you want these lipids without having the time to wait for such a thing to be implemented, it should be rather straightforward to build these lipids (i.e. make new entries in the charmm27.ff/lipids.rtp file) by manual "gluing" together the individual constituents. For example, in the top file of the CHARMM ff (version c32b1), this information is given for building a DPPC: """ !The following two residues (PALM and PCGL) and the two subsequent !patches (EST1 and EST2) are a modular way to create DPPC. !See the comments with EST1 and EST2 for more details. adm jr., Jul 99 """ > Thanks a lot , > Yuanyuan Wang By the way I'm only a poor PhD student, no professor :) Regards, Pär Bjelkmar <><><><><><><><><><><><><><><><><><><><><> Pär Bjelkmar, Ph.D. student Stockholm Center for Biomembrane Research (CBR), Stockholm Bioinformatics Center (SBC), Department of Biochemistry and Biophysics (DBB), Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><><><><> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?
Hi, The script I've used for the CHARMM port might be of use to you, e-mail me offlist if interested. It's not the greatest piece of code (in pyhon) and it is written to parse version c32b1. My experience is that the force field structure alters quite a bit between CHARMM releases. So writing a script for general porting of CHARMM ff to GMX is probably quite a task. Regards, Pär Bjelkmar > Message: 3 > Date: Mon, 23 Aug 2010 14:51:30 -0400 > From: fang yuan > Subject: Re: [gmx-users] Does anyone know how to get the file > charmm_gromacs.tar.gz? > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, I have the same problem, I need to implement the general CHARMM > forcefield in gromacs, so I need to know how to convert the rtf files into > rtp files in gromacs > <><><><><><><><><><><><><><><><><><><><><> Pär Bjelkmar, Ph.D. student Stockholm Center for Biomembrane Research (CBR), Stockholm Bioinformatics Center (SBC), Department of Biochemistry and Biophysics (DBB), Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><><><><> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Problem with Charmm in gromacs
Hi Fabrizio, Could you send me the input files and I'll take a look at it. You can send it to bjelk...@cbr.su.se Regards, Pär Bjelkmar 29 apr 2010 kl. 16.34 skrev gmx-users-requ...@gromacs.org: > Message: 3 > Date: Thu, 29 Apr 2010 10:33:53 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Problem with Charmm in gromacs > To: "Gromacs Users' List" > Message-ID: <4bd998d1.6010...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Fabrizio Marinelli wrote: >> Here it is my .mdp file, i attach you also the topology file, just to be >> more specific the one that are 0 are the SR interactions, thank you very >> much. > > For diagnostic purposes, can you re-process your structure using a different > force field and try again? If the energies are still coming up zero, then > there > may be something wrong in the code as a whole, otherwise it is specific to > the > CHARMM force field. Either way, I'm out of my league on this one :) Maybe a > developer can comment. > > -Justin > >> Fabrizio >> >> title= Teaa MD >> cpp = /lib/cpp >> include = >> integrator = md >> comm_mode= Linear >> nstcomm = 10 >> tinit= 0 >> comm-grps= System >> dt = 0.002 >> nsteps = 600 >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 5000 >> nstvout = 5000 >> ; Output frequency for energies to log file and energy file = >> nstlog = 500 >> nstenergy= 500 >> nstxtcout= 500 >> xtc-precision= 10 >> xtc_grps = System >> energygrps = System >> pbc = xyz >> nstlist = 5 >> epsilon_r= 1. >> ns_type = grid >> coulombtype = pme >> vdwtype = Cut-Off >> fourierspacing = 0.12 >> ; EWALD/PME/PPPM parameters >> pme_order= 4 >> ewald_rtol = 2.2e-05 >> epsilon_surface = 0 >> optimize_fft = yes >> rlist= 1.2 >> rcoulomb = 1.2 >> rvdw = 1.2 >> tcoupl = Berendsen >> tc-grps = System >> tau_t= 1.0 >> ref_t= 298 >> pcoupl = Berendsen >> pcoupltype = isotropic >> tau_p= 2.5 >> compressibility = 4.5e-5 >> ref_p= 1.0 >> ; Dielectric constant of reaction field = >> epsilon_rf = 80.0 >> gen_vel = yes >> gen_temp = 298 >> gen_seed = 173529 >> constraints = all-bonds >> constraint_algorithm = lincs >> shake_tol= 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 4 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> user1-grps = System >> ; Non-equilibrium MD stuff = >> acc-grps = >> accelerate = >> freezegrps = >> freezedim= >> cos-acceleration = >> >> >>> >>> Fabrizio Marinelli wrote: >>>> Hi all, >>>> I have downloaded the latest git version of gromacs (yesterday) in which >>>> it is possible to use the charmm27 force field, I constructed the >>>> topology >>>> for my protein using the pdb2gmx program, everything goes ok also with >>>> the >>>> solvation, but then when i run the MD i notice that coulomb and LJ >>>> interaction are 0 and also the protein consequently unfold. >>>> Did any of you found this kind of problem? Could some of you rpopose >>>> eventually a solution? >>> Can you post your .mdp file? >>> >>> -Justin >>> >>>> Thanks in advance, >>>> Fabrizio >>> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: ffcharmm27 for HEME
Hi, 15 apr 2010 kl. 11.11 skrev Ramachandran G: > Hello Par: >Using the latest git i could able to work on my oxy-hemoglobin system > with new gromacs version 4.0.5 successfully. CHARMM is not supportd in version 4.0.5, you probably mean the developer version? > But since my new gromacs version was not installed in parallel i tried using > older version of gromacs 3.3.1 which was installed in parrallel. While doing > grompp to get the *.tpr file, i am getting the below error. > - > Program grompp, VERSION 3.3.1 > Source code file: topdirs.c, line: 103 > > Fatal error: > Invalid dihedral type 9 > -- This is because we have made changes in the source code to allow for the CHARMM ff (we added a new dihedral type, see paper, that is causing this particular error). So, you have to run with the developer git version. Regards, Pär > > I am planning to install the newer gromacs version also in parallel but in > the mean time i also wanted to rectify the above error, if i can. Thank you. > > Rama > > > On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar wrote: > Hi, > > I have now added the charmm files to git head and the protein and lipid parts > should work at least. Simply check out the latest git and the charmm > parameters should show up in pdb2gmx. > > /Pär > > 11 mar 2010 kl. 03.04 skrev Ramachandran G: > >> Hello Bjelkumar, >> Thanks for your reply. I will wait until you add the new force >> field to the git. >> >> regards, >> rama >> >> On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar wrote: >> Hello, >> >> I have that on my schedule for next week. That is to add the new force field >> format to the git source code tree. Until then you could use the old format >> if you checkout a previous version of the source code. I guess you know >> about git otherwise there's some info here >> http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage >> >> So start by getting a copy of the latest _developing_ version (git head) of >> gromacs source code: >> $ git clone g...@git.gromacs.org:gromacs.git >> The force field files were update in end of January to you could checkout a >> version from Jan 27 by: >> $ git checkout d80138d720fd41a5005238adecd5bfd5400e524c >> >> then compile. Now it should work if you got the HEME parameters from Michel. >> Alternatively you wait until end of next week when I think I have had time >> to add the new force field format to the git head. >> >> Good luck! >> /Pär >> >> 1 mar 2010 kl. 21.21 skrev Ramachandran G: >> >>> Dear Pär Bjelkmar, >>> After getting help from Michel Cuendet still i am facing problem >>> and i >>> understood that in groamcs latest version 4.0.x problems may come due to >>> CMAP. >>> He suggested me to seek your help. Could you help me to get new toplogy >>> format charmm files which can adapt the HEME sections to that. >>> Thank you. >>> >>> Rama >>> >>> -- Forwarded message -- >>> From: Michel Cuendet >>> Date: Fri, Feb 26, 2010 at 1:03 PM >>> Subject: Re: ffcharmm27 for HEME >>> To: Ramachandran G >>> >>> >>> >>> Dear Mr. Ramachandran, >>> >>> This means you are using grompp from the distribution version 4.0.x. >>> This version of gromacs does not know about the CMAP forcefield term. >>> You have two options : >>> >>> 1) Deactivate CMAP. This would be equivalent to using the charmm22 ff >>> instead of the charmm27, which many people consider fine. To do this, >>> edit the file ffcharmm27.rtp and delete all [cmap] sections. This >>> _should_ work. >>> >>> 2) Download the git development version, which knows how to handle CMAP. >>> I know they have been changing topology formats in the latest versions, >>> but I hope it is still able to read the old topologies. Otherwise, you >>> will have to ask Par Bjelkmar for the charmm files in the new topology >>> format, and adapt the HEME sections to that. >>> >>> Sorry it is a bit messy at the moment. But everything should become part >>> of the gormacs4.1 distribution. >>> >>> Bye, >>> Michel >>> >>> Ramachandran G wrote: >>> > Dear Mr. Michel, >>> >
[gmx-users] Re: charmm lipid simulation and vsites
Hello David, I send answer to the gromacs mailing list also. 12 apr 2010 kl. 17.51 skrev David Caplan: > I am still experimenting with the CHARMM27 support in Gromacs. I am > using a very recent git version (from last week). > > Currently, I'm trying to equilibrate a membrane bilayer with virtual > sites. The membrane is DPPC with the Sonne et al. parameters (for zero > surface tension): > Sonne et al. Reparameterization of all-atom > dipalmitoylphosphatidylcholine lipid parameters enables simulation of > fluid bilayers at zero tension. Biophys J (2007) vol. 92 (12) pp. > 4157-67 > > I am not so familiar with vsites, but I have read the documentation > and I saw you used vsites in your recent paper. Have you used vsites > with membrane simulations using CHARMM27? No, I have not but it should be straight forward. > If so, what kind of pressure > coupling do you use? is any surface tension applied? > If you have an example MDP that you used for this I would love to take > a look at it. I would use semiisotropic Berendsen for equilibration and perhaps switch to Parrinello-Rahman during production but when it comes to surface tension and CHARMM simulations I'm afraid I don't have any experience. Guess you have to read the cited paper carefully to figure this out. > > Also, do you typically run your CHARMM27 simulations using Langevin dynamics? No, not when you have explicit solvent. /Pär -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Charmm port files for Gromacs
Hi, I answer to the gmx-users mailing list and I would be pleased if further correspondence is done there. It's an installation issue because the CMAP directive is not recognized by pdb2gmx. Seems like you are running version 4.0.7 and that is then the explanation. You need to run with the developing version (because it is has not been released yet) from git to run with CHARMM. There're installation instructions on the gromacs webpage. Worth to note: 1. more information about the port is available in paper by yours sincerely and coworkers (Bjelkmar et al. Journal of Chemical Theory and Computation, 2010) 2. the force field format has been changed and the most recent version of the force field (complying to this new format) was added to the source. I.e. you should use those files (not the ffcharmm27* files from my homepage). Regards, Pär Bjelkmar 5 apr 2010 kl. 17.51 skrev Smiruthi Ramasubramanian: > Hi Pär, > > I've been testing the charmm27 forcefield and keep getting this error: > > Program pdb2gmx, VERSION 4.0.7 > Source code file: resall.c, line: 344 > > Fatal error: > in .rtp file in residue cmap at line: > -C N CA C +N > > I couldn't find a plausible solution in the gmx forums and was wondering if > there was a problem in the installation. I am not using ACE or other capping > residues in the pdb. > > > Thanks, > Smiruthi > > > > On Thu, Mar 18, 2010 at 6:00 AM, Pär Bjelkmar wrote: > Hello Smiruthi, > > Nice to hear that you're interested in the port. First, you need to run with > the git head version (see instructions on my page > www.dbb.su.se/User:bjelkmar/Ffcharmm or on gromacs.org). Since about one > month, the version of the force field (version 1.1) on this homepage has not > been working with git head because the force field format was changed in > GROMACS. Yesterday, I committed the updated version of the CHARMM parameters > to the version-tracking program (git) in the head branch so it should work > now. However, this is still a somewhat work-in-progress force field port > (especially in the nucleic acid part) and there _might_ be changes (although > minor ones for sure) until GROMACS 4.1 is released. The protein and lipid > parts should be fairly safe to use though. > > Regards and good luck, > Pär Bjelkmar > > 16 mar 2010 kl. 20.20 skrev Smiruthi Ramasubramanian: > >> Hi Pär, >> >> I am a Phd student in Rudy Lab (http://rudylab.wustl.edu/) at Wustl. We are >> working on comparing NAMD and Gromacs umbrella sampling related to passage >> of ions through membrane proteins. Could you please send me the Charmm port >> files listed in http://www.dbb.su.se/User:Bjelkmar/Ffcharmm . Unfortunately, >> I keep getting "Internal Error" and I am not sure if it is a problem at our >> end or if your server is temporarily down. >> >> I apologize for any inconvenience and appreciate the help. >> >> Thanks, >> Smiruthi > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: CHARMM TIP3-Water with GMX
Hi Stephane, > I am doing some tests with the CHARMM port in GROMACS. Before to start > more extensive simulations with this ff > I have performed a short run of 1000 TIP3-CHARMM water molecules in a > cubic during at T=300 K and P=1.015 bar with v-rescale and PR as > thermostat and barostat. I have used the VERSION > 4.0.99_development_20090927 of GMX. good to hear that you could reproduce our results. > > Moreover, since I am not a power user of GROMACS, I don't know how to > translate in GROMACS directives the sentence given in JCTC paper " using > a short-range cutoff of 1.2 nm, and van der Waals interactions were > switched off between 1.0 to 1.2 nm". This means coulombtype = PME, rcoulomb = 1.2, vdw-type = switch, rvdw-switch = 1.0, rvdw = 1.2. > And by consequence what are the > corrects coulomb and vdw parameters for simulations of CHARMM ff ? This you should be able to figure out from the CHARMM ff papers. According to the CMAP paper (MacKerell et al. Journal of Computational Chemistry 2004) they used real-space (short-range) cutoff of their electrostatic calculations (using PME) of 8.5 Å, and the LJ were switched of between 7.5 to 8.5 Å and their neighbor lists had a cutoff of 10.5 Å. Remember that we performed the testing (comparing the energy terms) in the paper without cut-offs. /Pär-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] perl scripts to convert CHARMM ff in GROMACS
Hi, I wasn't fast enough answering this but I sent you an e-mail off-list. And as I said, when you get this to work you can put this on the Downloads->User contributions->Force fields on gromacs.org. Regards, Pär Bjelkmar > Hi, > > With the Mark Abraham's scripts and advices, I have finally resolved my > problems. > > Thank you and see ya on the list > > Stéphane <><><><><><><><><><><><><><><><><><> Pär Bjelkmar, PhD student Stockholm Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: about beta port of C27 FF to gromacs
Hi, >>> --- >>> Program pdb2gmx, VERSION 4.0.7 >>> Source code file: resall.c, line: 344 >>> >>> Fatal error: >>> in .rtp file in residue cmap at line: >>> -C N CA C +N >>> :q! >>> --- > > Did somebody use vi to edit this file and accidently inserted rather than > quit? Sharp eye! Nop I didn't change anything, this is how it looked in the original message. /Pär-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: about beta port of C27 FF to gromacs
Hi Alexandar, I redirected my answer to the gmx-users mailing list so it's available to all users. 23 jan 2010 kl. 22.41 skrev Alexandar T Tzanov: > Hi Par, > > I downloaded your 'Charmm to Gromacs port v1.1" and tried it on my simple > system - NATMA (ACE-TRP-NAC total 36 atoms). I used > > pdb2gmx -f natma.pdb -ff charmm27 -o natma1.pdb -ter -water tip3p > > and got: > > Analyzing pdb file > There are 1 chains and 0 blocks of water and 3 residues with 36 atoms > > chain #res #atoms > 1 'X' 3 36 > > All occupancies are one > Opening library file /usr/local/gromacs/share/gromacs/top/ffcharmm27.atp > Atomtype 1 > Reading residue database... (ffcharmm27) > Opening library file /usr/local/gromacs/share/gromacs/top/ffcharmm27.rtp > Residue 1 > --- > Program pdb2gmx, VERSION 4.0.7 > Source code file: resall.c, line: 344 > > Fatal error: > in .rtp file in residue cmap at line: > -C N CA C +N > :q! > --- > > > I am wondering if there is a bug in a code or I am doing something wrong. > My gromacs is latest available - 4.0.7 Well, the CHARMM source is not available in version 4.0.7 but in git head (it will be part of version 4.1) so you have to pull the latest git source. Having said that, there might very well be something wrong when using ACE termini since it has to be treated a bit specially in GROMACS (i.e. as a residue rather than in the termini db, as is also the case in the amber port) and this particular termini has not been tested by us. I don't know what residue/termini NAC is but nothing with that name is present in the CHARMM top file I'm parsing. To use a ACE termini, you need to have the coordinates of the ACE also in the input file (since it's a residue by itself and will not be generated by pdb2gmx) and it has to have it's own residue number. Then you select the None N-"termini". (Correct me somebody if I'm wrong). You could send me your input coordinate file if this doesn't help and I'll take a look at it. Regards, Pär Bjelkmar > > > Thanks > > Alex > === > Alexander Tzanov > > New York University > Department of Chemistry > 100 Washington Square East, Room 1001U > New York, NY 10003 > Phone: 212-998-3589 > Fax: 212-995-4475 > Email: alex.tza...@nyu.edu > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CHarmm and popc membrane
Hi, > I still don't see it (see below), is this [no]chargegrp new in the cvs ? > I'm pretty sure that you're not referring to [no]lys, etc. Yes, that seems to be the case indeed. I've got it in my 'cvs' installation but not in my 4.0.7. /Pär-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")
Hi Chris, > > I believe that the latest response had the wrong subject, so I am > changing it back. > > Pär, two comments: > First, does that option really exist? > > $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z > 2>&1; cat z|grep nochargegrp|wc -l > The name flag is listed as [no]chargegrp > > Second, I am not entirely convinced that one can discount the need for > gromacs-style charge groups. When CHARMM includes an atom in the > cutoff, it includes the entire charge group, but that doesn't mean the > algorithms of CHARMM and gromacs are entirely the same That's why I said if you know what you're doing :) > > I gather that the large charge group listed below is the one that is > spurring the message: > > GROUP ! H31 > ATOM NNTL-0.60 ! | > ATOM C11 CTL2 -0.10 ! H33-C13-H32 > ATOM C12 CTL5 -0.35 ! | > ATOM C13 CTL5 -0.35 ! H21 | H43 > ATOM C14 CTL5 -0.35 !|| | > ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+) > ATOM H12 HL 0.25 !|| | > ATOM H21 HL 0.25 !H23 | H41 > ATOM H22 HL 0.25 ! | > ATOM H23 HL 0.25 ! | > ATOM H31 HL 0.25 ! | > ATOM H32 HL 0.25 ! H11-C11-H12 > ATOM H33 HL 0.25 ! | > ATOM H41 HL 0.25 ! | > ATOM H42 HL 0.25 ! | > ATOM H43 HL 0.25 ! | Yes, and probably one charge group in the arginine residue(s). /Pär-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Missing Residues are list ind pdb file
Hi, Note, that this is indeed the size of the charge groups in the CHARMM force field. You could run pdb2gmx -nochargegrp if you know what you're doing. Regards, Pär Bjelkmar > I think the notes from grompp are pretty clear. You need to redivide > your charge groups so that they contain fewer atoms. You can do this > in the .top or .itp file and you can find out how to do that in the > manual. Feel free to post your original and charge-group-modified > topologies back here if you want people to take a look at them. > > Chris. > > -- original message -- > > I am trying to equilibrate a POPC membrane with 128 POPC molecules, but > grompp gives out the following notes and minimization with mdrun does not > work. The output on screen of mdrun comes out like this: > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 10. > Potential Energy = 1.4422483e+17 > Maximum force =inf on atom 4082 > Norm of force =inf > > And grompp notes are: > NOTE 2 [file topol.top, line unknown]: > The largest charge group contains 12 atoms. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: charmm, cmap and gromacs 4.1
Hi again, > Yes, I did git pull and the output is this: > > remote: Counting objects: 9, done. > remote: Compressing objects: 100% (5/5), done. > remote: Total 5 (delta 4), reused 0 (delta 0) > Unpacking objects: 100% (5/5), done. >> From git://git.gromacs.org/gromacs > c358dce..b493dbb master -> origin/master > Already up-to-date. > > Still charmm does not work. Is there something wrong about the way I > included the forcefield files in the top directory, should I have changed > something else? Hmmm, seems like you have done everything correct. If you have not renamed the force filed files the entry in FF.dat should look like this: ffcharmm27 CHARMM 27 all-atom force field and don't forget to increase the number of the first line in the file either! You could also try to run pdb2gmx with the flag -ff ffcharmm27 and see if that works (instead of selecting it interactively from FF.dat). Also take a look in the pdb2gmx output and see if any of the ffcharmm27 parameter files (I think ffcharmm27.rtp should be the first one read by pdb2gmx) are read. I did the gromacs installation myself yesterday and I got it to work. Regards, Pär -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] charmm, cmap and gromacs 4.1
Hi, > Hello. Thank you for the git repository tip, but I don't think it worked > out. > I tried using "git clone git://git.gromacs.org/gromacs.git". Did you do git pull? > From the > gromacs directory that git created I ran "./bootstrap" and then ./configure > .etc. > I inserted the ffcharmm files into the ~GROMACSPATH/top directory and edited > the FF.dat file to include a eleventh line with the ffcharmm27 forcefield. > Finally, when I ran pdb2gmx and chose ffcharmm27 as a forcefield pdb2gmx > gave the following error: > > Fatal error: > in .rtp file in residue cmap at line: >-CNCAC+N /Pär >>> >>> I wanted to use charmm forcefield on gromacs (am using 4.07) but when I >> try >>> using this forcefield gromacs tells me that there is a problem with CMAP. >> I >>> read that gromacs 4.1 is coming with charmm forcefield as well. If that >> is >>> true, when is gromacs 4.1 coming and how can I use charmm FF with gromacs >>> for now? >> The code supporting CHARMM is in git master (see >> http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial) and will, as you >> say, be included in version 4.1. Download CHARMM force filed files v1.1 from >> http://www.dbb.su.se/user:bjelkmar/ffcharmm. They will, of course, also be >> included with 4.1. >> >> Actually, I got the notification yesterday that a paper describing this >> implementation will be published in JCTC. >> >>> Would it be better to wait for gromacs 4.1? >> There might be some minor changes until 4.1 but the current (CHARMM-) code >> (in git master) is tested and is working well. Once version 4.1 is released >> I would recommend you to update to that version. >> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] charmm, cmap and gromacs 4.1
Hi Stefan, > Message: 2 > Date: Mon, 11 Jan 2010 19:48:53 -0200 > From: Stefan Hoorman > Subject: [gmx-users] charmm, cmap and gromacs 4.1 > To: gmx-users@gromacs.org > Message-ID: > <3078c1dd100348m6fb3d96epcc9202869d7b3...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I wanted to use charmm forcefield on gromacs (am using 4.07) but when I try > using this forcefield gromacs tells me that there is a problem with CMAP. I > read that gromacs 4.1 is coming with charmm forcefield as well. If that is > true, when is gromacs 4.1 coming and how can I use charmm FF with gromacs > for now? The code supporting CHARMM is in git master (see http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial) and will, as you say, be included in version 4.1. Download CHARMM force filed files v1.1 from http://www.dbb.su.se/user:bjelkmar/ffcharmm. They will, of course, also be included with 4.1. Actually, I got the notification yesterday that a paper describing this implementation will be published in JCTC. > Would it be better to wait for gromacs 4.1? There might be some minor changes until 4.1 but the current (CHARMM-) code (in git master) is tested and is working well. Once version 4.1 is released I would recommend you to update to that version. Regards, Par Bjelkmar <><><><><><><><><><><><><><><><><><> Pär Bjelkmar, PhD student Stockholm Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] RE: Does Gromacs support CHARMM force field now?
Hi, I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? The files are there unofficially (that's why they're not included in the ff.dat file) and in an old version. You could try out the charmm27 parameters with CMAP support by downloading the latest version of the source code in git master and use the latest files, which I can provide you with (send an e-mail to me and I'll give them to you). The CHARMM ff (for proteins and lipids at least) will be officially supported in upcoming Gromacs version 4.1. Regards, Pär Bjelkmar-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CMAP request
Hi Supid, We are trying to convert CHARMM force field for MTSSL (a small molecule which is used as EPR label) into gromacs format. But in CHARMM they have CMAP. I checked the gromacs mailing archive and found that there is a gromacs CVS where CMAP implementation is done. Yes, the code is in the git master branch and is officially released as of version 4.1. You'd need a rtp entry of MTSSL for this to work with CMAP terms defined as for the amino acids (you can get the CHARMM27 ff files supporting CMAP from me if you send me an e-mail). Don't know if the CHARMM community has generalized the use of the CMAP term for something else than a peptide though. I mean CMAP is a correlation term between protein backbone phi and psi angles and MTSSL doesn't seem to be a peptide, right? It will be very helpful for us if we get a copy of the code. /Pär <><><><><><><><><><><><><><><><><><> Pär Bjelkmar, PhD student Stockholm Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><> ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] force field
Hi, leila karami wrote: I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. For AMBER, download the ffamber ports: http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER CHARMM is not yet officially supported, but will be in a future release (4.1?) Yet that's correct. If you want to try out the beta version of the ff send me an e-mail Leila. <><><><><><><><><><><><><><><><><><> Pär Bjelkmar, PhD student Stockholm Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><> ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] question about all atoms lipid molecule
Hi, I need to do an all atom simulation for dppc bilayer . You are right the dppc molecule file that i have has PALM and PCGL residues. Well, I don't know where you got the dppc molecule from, I thought you said you didn't have any DPPC structure with hydrogens? Anyway, I'll send you the current version of the charmm force field for GROMACS (in a separate e-mail) but I'm afraid I cannot help you in building the residue. I think it might be quite a lot of work if you don't know how CHARMM is doing it. My suggestion is that you search/ask the CHARMM mailing list for how DPPC is constructed. I will like to try to set up the charmm FF for gromacs. But I dont have the FF files with me, neither do i have the programs. Could you send me a tutorial or some reference link too ( if you know of any). What you need for running CHARMM ff in GROMACS are the files I'll send you and the latest version of the source code (i.e. do a git pull and recompile). /Pär___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] question about all atoms lipid molecule
Hi, 15 okt 2009 kl. 07.08 skrev gmx-users-requ...@gromacs.org: The reason I am asking this is because it will require me to create gromacs compatible FF files of the Charmm FF . I did find two perl scripts which can do probably handle that but i am wondering if the compatible FF are already up on gromacs website somewhere. No, it is not available on the gromacs website yet. You can get the current parameter files from me if you'd like to try it out. I'm afraid the DPPC lipid in CHARMM is created by combining the PALM and PCGL residues and some patches so if you know how that works in CHARMM you might be able to create the DPPC residue. No one ever said life was easy :) CHARMM support is under development, you can get the source via the git repositories, but I don't know its current status. As Justin is saying, CHARMM will be supported as of version 4.1. The source code is there in git master branch but you need to get the ff files from me. I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. /Pär Bjelkmar <><><><><><><><><><><><><><><><><><> Pär Bjelkmar, PhD student Stockholm Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><> ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Current status of CMAP
The status of charmm with cmap is that it is implemented and present if one does git pull. The force field files of the distribution is outdated and should not be used. Instead interested users should contact me for the latest ones (different from the ones available from "my" webpage, http://www.dbb.su.se/User:Bjelkmar/ffcharmm). We have tested the code and are pretty convinced that the major parts for proteins are correct (0-step energies are correct compared to charmm in charmm). However, we're still working with it and testing termini, virtual sites, implicit solvent, etc. Our aim is to release it with gromacs 4.1 (although I have broken such "promises" before on this mailing list...). Mark A: Actually I'm following the list but your suspicion is a valid one regarding the number of posts I have made... :D Regards, Pär Bjelkmar 7 aug 2009 kl. 17.39 skrev gmx-users-requ...@gromacs.org: Hi all, I know this has been up on the list before, but I haven't been able to get some definite answer - What's the current status of the implementation of CHARMM-type CMAPs? I note that people (especially P. Bjelkmar as it seems) have done a great job implementing the other peculiarities of the CHARMM force fields, but it's still that final piece missing. There are several references to CMAP in the source code, but I guess it's not fully implemented yet. I just wonder if it will be ready anytime soon? I would be glad to help anyway I can, at least by doing some testing. Best regards, Jakob Wohlert <><><><><><><><><><><><><><><><><><> Pär Bjelkmar, PhD student Stockholm Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University Tel:+46-8-16 2746 Fax: +46-8-15 3679 E-mail: bjelk...@cbr.su.se Home: http://www.dbb.su.se/User:Bjelkmar <><><><><><><><><><><><><><><><><><> ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problem in increasing lipid bilayer size and to know about net charge on protein
Hi Nitu, 9 apr 2009 kl. 08.56 skrev gmx-users-requ...@gromacs.org: 2. I want to know the net charge present on my protein can u suggest me how can it become possible . Based on the protonation states and the termini you use in pdb2gmx the total charge is reported to stdout. Regards, Pär ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [[gmx-users] genion error!]
Maybe you forgot to delete the waters that were removed in the ionization process? /Pär > Dear users: > I want to prepare protein simulation on 0.15mol/l salt > concentration,I use > genion command to add ions,After genion,I change cln.top file last > line to NA+ > 61,CL- 41. >When I execute grompp ,there are warning : > > Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) > > (more than 20 non-matching atom names) > WARNING 1 [file "cln.top", line 9059]: > 102 non-matching atom names > atom names from cln.top will be used > atom names from cln_b4em.gro will be ignored > > I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o > minim_traj.trr -c > minimized.gro -e minim_ener.edr",There are some error: > Fatal error: > Too many LINCS warnings (10190) - aborting to avoid logfile runaway. > This normally happens when your system is not sufficiently > equilibrated,or if you > are changing lambda too fast in free energy simulations. > If you know what you are doing you can adjust the lincs warning > threshold > in your mdp file, but normally it is better to fix the problem. > > I don't know what happen ,could somebody tell me? > Thank you very much! > > > > pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top > editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 > genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top > grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr > genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral > grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr > mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e > minim_ener.edr > grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr > mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c > md_final.gro -e > md_ener.edr > > > > > -- > Qiang Zhong > Key Lab of Agricultural Animal Genetics, Breeding and Reproduction > of Ministry of Education > College of Animal Sciences and Technology > Huazhong Agricultural University > Wuhan,Hubei, 430070 > PR China > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- * Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] information on Na Channels in lipid bilayers ?
Hi Sridhara, One fairly recent paper (about a year old) on the structure of a Na+/K+ conducting channel is: Shi, Ye, Alam, Chen & Jiang, Nature 440 (23):570-4. /Pär On Thu, 2007-03-22 at 12:00 +0100, [EMAIL PROTECTED] wrote: > Message: 1 > Date: Wed, 21 Mar 2007 15:11:15 -0400 > From: "Viswanadham Sridhara" <[EMAIL PROTECTED]> > Subject: [gmx-users] information on Na Channels in lipid bilayers ? > To: "GROMACS list" > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello everyone, > > I tried looking to find papers / information on any sodium channels > embedded in bilayers. It would be great if someone can direct me > regarding this. > > I could find information on potassium channels embedded in lipid > bilayers. Ofcourse, I could also find lot of information on sodium > permeability in Alamethicin and Gramicidin A. But, not much help with > sodium channels. > > Looking forward to your response. > > Regards, > Viswam. > > -- > Viswanadham Sridhara, > Research Assistant, > Old Dominion University, > Norfolk, Va-23529. -- * Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Official charmm support
I appreciate your suggestion! It shouldn't be hard; a quick look tells me there are only some unconventional "tags" (compared to the standard charmm ff defs) in this ff definition the porting script has to cope with. I'll address the matter as soon as we're done with the port supporting cmap. It probably won't be tested though... Cheers, Par Bjelkmar > I would like to suggest that you include the > carbohydrate force field of J Brady (CSFF). Here are > some references and download sites > > Journal of computational chemistry 2002, vol. 23, > no13, pp. 1236-1243 > http://people.cs.uct.ac.za/~mkuttel/downloads.html > > Thanks > > Gil Claudio > > > > Dear gromacs users, > > > > I'm a new PhD student in Erik Lindahl's group and we > > are currently > > working on an "official" implementation of the > > charmm ff in gromacs > > which also supports CMAP. There's still some more > > work needed on the > > CMAP part but we intend to have a (thoroughly) > > tested version of the > > protein lipid charmm force field completed New > > Yearish. The problem with > > the multiple entries (see thread "CHARMM force field > > implementation in > > Gromacs" in gmx-users) of certain (proper) dihedrals > > where at least one > > has a multiplicity > 5 is also supported by adding a > > new dihedral > > type. > > > > The testing of other system types is something we > > would like to > > outsource on the gromacs users interested in them > > since we don't > > normally study other systems than protein-lipid ones > > in the group. If > > you have a specific system you would like to test in > > our new gromacs > > version and cannot wait until it's released, please > > contact me and we > > could arrange something. > > > > Yours, > > Pär > > -- > > > * > > Pär BjelkmarStockholm Center for > > Biomembrane Research > > Tel: +46-8-16 2746 Dep of Biochemistry and > > Biophysics > > Fax: +46-8-15 3679 Stockholm University > > [EMAIL PROTECTED] 10691 Stockholm, Sweden > > * > > > > > Want to start your own business? > Learn how on Yahoo! Small Business. > http://smallbusiness.yahoo.com/r-index > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- * Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Official charmm support
Dear gromacs users, I'm a new PhD student in Erik Lindahl's group and we are currently working on an "official" implementation of the charmm ff in gromacs which also supports CMAP. There's still some more work needed on the CMAP part but we intend to have a (thoroughly) tested version of the protein lipid charmm force field completed New Yearish. The problem with the multiple entries (see thread "CHARMM force field implementation in Gromacs" in gmx-users) of certain (proper) dihedrals where at least one has a multiplicity > 5 is also supported by adding a new dihedral type. The testing of other system types is something we would like to outsource on the gromacs users interested in them since we don't normally study other systems than protein-lipid ones in the group. If you have a specific system you would like to test in our new gromacs version and cannot wait until it's released, please contact me and we could arrange something. Yours, Pär -- ********* Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
