[gmx-users] About Solvation of Lipid Protein
Dear Justin Thank you for your Previous reply I am following your Protein-lipid Tutorial ( KALP peptide in DPPC) In your tutorial How many Number of Water Molecules you needed to solvate Lipid -protein When I solvate The Number of Water Molecules are 57647 Is it Too high Or Ok Thanks In Advance -- 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] Conceptual question about the representation of dihedral angles in Gromacs
On 2012-10-27 03:02, Andrew DeYoung wrote: Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydrogens H1, H2, and H3 are bonded to C1. Hydrogens H4, H5, and H6 are bonded to C2. I would like to account for all possible H*-C1-C2-H* dihedral angles. From organic chemistry, I know that the rotational barrier of ethane is approximately 2.9 or 3 kcal/mol (see, for example, http://research.cm.utexas.edu/nbauld/teach/ethane.html). In the OPLS-AA force field, I have found parameters for the dihedral HC-CT-CT-HC: HC CT CT HC 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 ; hydrocarbon *new* 11/99 If I plot the potential energy V for these RB parameters on a plotter, it appears that the barrier height is about 0.9 kcal/mol (I converted from kJ/mol by dividing by 4.184). My question is, do the above parameters correspond to only a _single_ H-C-C-H dihedral (for example, H1-C1-C2-H4)? If so, then I will need to specify H1-C1-C2-H5 and H1-C1-C2-H6 in addition to H1-C1-C2-H4, I think. By doing so, I will be essentially adding 3 different plots: one for H1-C1-C2-H4, one for H1-C1-C2-H5 (phase-shifted by 120 degrees relative to H1-C1-C2-H4), and one for H1-C1-C2-H6 (phase-shifted by 240 degrees relative to H1-C1-C2-H4). In this way, the total barrier height will be 0.9 + 0.9 + 0.9 = 2.7 kcal/mol, approximately consistent with common knowledge from organic chemistry. Is this correct? In other words, the dihedral parameters represent a _single_ dihedral (for example, H1-C1-C2-H4), and _NOT_ a group of dihedrals (for example, H1-C1-C2-Hx where x = 4, 5, 6). Only by considering all possible dihedrals do we get the correct potential overall energy landscape. One conceptual problem I have with this, though, is that I get the 2.7 kcal/mol barrier height only by considering H1-C1-C2-Hx, where x = 4, 5, and 6. But I also will include H2-C1-C2-Hx and H3-C1-C2-Hx in my topology (where x = 4, 5, and 6 in each case). Does this mean that when I consider all possible dihedrals Hy-C1-C2-Hx (x = 4, 5, 6; y = 1, 2, 3), the overall barrier height will be 3 * 2.7 = 8.1 kcal/mol instead of 2.7 kcal/mol? All dihedrals are included in OPLS/AA, so you get 9 different ones, all in phase as well. On top of that is the Coulomb and Van der Waals interaction between the H, which will increase the barrier height (because the atoms are closest there). In other words the barrier is way too high. Thank you! Andrew -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Conceptual question about the representation of dihedral angles in Gromacs
Dear Andrew, I am a beginner! However, I would like to record my interpretation of the concept you're confused about and evaluate it by what experts will comment later. I am pretty sure your first calculation of 2,7 kcal/mol is correct, however, since ethane is symmetrical molecule you don't need to perform the second calculation so as to take into account all the dihedral interactions. I am not sure how far are you familiar with quantum mechanics and the orbital theory of two and above electron atoms! Actually, as you cannot distinguish between electrons there, in the case of ethane you cannot distinguish between the hydrogen atoms and thus, every time, any Hx meets any of Hy s makes no difference in calculation of your barrier height and are all the same. I hope I could transfer my knowledge to you. Lets see what others will come up with. Cheers On Sat, Oct 27, 2012 at 4:32 AM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydrogens H1, H2, and H3 are bonded to C1. Hydrogens H4, H5, and H6 are bonded to C2. I would like to account for all possible H*-C1-C2-H* dihedral angles. From organic chemistry, I know that the rotational barrier of ethane is approximately 2.9 or 3 kcal/mol (see, for example, http://research.cm.utexas.edu/nbauld/teach/ethane.html). In the OPLS-AA force field, I have found parameters for the dihedral HC-CT-CT-HC: HC CT CT HC 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 ; hydrocarbon *new* 11/99 If I plot the potential energy V for these RB parameters on a plotter, it appears that the barrier height is about 0.9 kcal/mol (I converted from kJ/mol by dividing by 4.184). My question is, do the above parameters correspond to only a _single_ H-C-C-H dihedral (for example, H1-C1-C2-H4)? If so, then I will need to specify H1-C1-C2-H5 and H1-C1-C2-H6 in addition to H1-C1-C2-H4, I think. By doing so, I will be essentially adding 3 different plots: one for H1-C1-C2-H4, one for H1-C1-C2-H5 (phase-shifted by 120 degrees relative to H1-C1-C2-H4), and one for H1-C1-C2-H6 (phase-shifted by 240 degrees relative to H1-C1-C2-H4). In this way, the total barrier height will be 0.9 + 0.9 + 0.9 = 2.7 kcal/mol, approximately consistent with common knowledge from organic chemistry. Is this correct? In other words, the dihedral parameters represent a _single_ dihedral (for example, H1-C1-C2-H4), and _NOT_ a group of dihedrals (for example, H1-C1-C2-Hx where x = 4, 5, 6). Only by considering all possible dihedrals do we get the correct potential overall energy landscape. One conceptual problem I have with this, though, is that I get the 2.7 kcal/mol barrier height only by considering H1-C1-C2-Hx, where x = 4, 5, and 6. But I also will include H2-C1-C2-Hx and H3-C1-C2-Hx in my topology (where x = 4, 5, and 6 in each case). Does this mean that when I consider all possible dihedrals Hy-C1-C2-Hx (x = 4, 5, 6; y = 1, 2, 3), the overall barrier height will be 3 * 2.7 = 8.1 kcal/mol instead of 2.7 kcal/mol? Thank you! Andrew -- 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 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: 回复： 回复： [gmx-users] ATP/ADP+Pi
Perhaps I was not too explicit. The parameterization details are on the first supplementary information file of the first paper I sent you. Here is the direct link: http://pubs.acs.org/doi/suppl/10.1021/jp905735y/suppl_file/jp905735y_si_001.pdf The parameters are built upon the already available ATP for 43A1, if i remember correctly. I hope this helps. Cheers, João On Sat, Oct 27, 2012 at 4:20 AM, 闪耀星空 382209...@qq.com wrote: Hello How to parameterize ATP, ADP and Pi ?my initiating structure has it,but the force field has not define the ATP,ADP,Pi and not recognition it .thanks -- 原始邮件 -- 发件人: 闪耀星空382209...@qq.com; 发送时间: 2012年10月27日(星期六) 中午11:03 收件人: Discussion list for GROMACS usersgmx-users@gromacs.org; 主题: 回复： [gmx-users] ATP/ADP+Pi Thanks for your help!! About these paper,I have just read them. In your paper,you selected 43a1 force field directly and did not talk about ATP/ADP+Pi parameters.But in my 43a1 force field ,the ATP parameters are exist,ADP and Pi are not.I use gromacs 4.5.5 versions. WHY?? Thanks!! -- 原始邮件 -- 发件人: João M. Damajmda...@itqb.unl.pt; 发送时间: 2012年10月26日(星期五) 晚上11:38 收件人: Discussion list for GROMACS usersgmx-users@gromacs.org; 主题: Re: [gmx-users] ATP/ADP+Pi Hello, At our group we have parameterized ATP, ADP and Pi to use with ABC transporters. Paper with the parameterization: http://dx.doi.org/10.1021/jp905735y Papers using the parameterized molecules: http://dx.doi.org/10.1002/prot.23023 http://dx.doi.org/10.1002/pro.650 http://dx.doi.org/10.1371/journal.pcbi.1002128 Cheers, João On Fri, Oct 26, 2012 at 4:12 PM, 闪耀星空 382209...@qq.com wrote: GMX-users: I am working with ATP+protein and ADP+Pi+protein in gromos43a1.ff force field,but I find only ATP parameters in the aminoacids.rtp file .Where can I achieve the ADP+Pi parameters ??? I wanted use the parameters from((http://www.pharmacy.manchester.ac.uk/bryce/amber) ) but it seemed unsuitable . What can I do??? Please help me with this. Thank you very much . -- 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] Type 9 dihedral in Gromacs topology
Hi, This question is a sequel of sorts to my earlier question about dihedral parameters in Gromacs (http://lists.gromacs.org/pipermail/gmx-users/2012-October/075860.html). I typically use the OPLS-AA force field. In OPLS-AA, dihedrals are usually specified with the Ryckaert-Bellemans function. In Table 5.5 on page 125 of Section 5.7 of the manual, such a Ryckaert-Bellemans function specification is called a type 3 dihedral. This is why there is a 3 in the function type column in the dihedral section of the OPLS-AA ffbonded.itp file. One can also use type 1 dihedrals, which, as shown in the manual, have the simple potential energy form V_d(phi_ijkl) = k_phi (1 + cos(n*phi - phi_s)). However, in the CHARMM force field ffbonded.itp file included in Gromacs, it seems that all of the [ dihedraltypes ] are specified using dihedral function type 9. Here is an example from the CHARMM ffbonded.itp: ; i j k l funcphi0cp mult C CT1 NH1 C 9 180.00 0.8368 1 If you have time, I have two questions about type 9 dihedral functions: (1) What is a type 9 dihedral? On page 74 of Section 4.2.12 of the manual, it says, For certain force fields, type 9 is useful. Type 9 allows multiple potential functions to be applied automatically to a single dihedral in the [ dihedral ] section when multiple parameters are defined for the same atomtypes in the [ dihedraltypes ] section. What does this mean? What does it mean to apply multiple potential functions to a single dihedral? Is this a fundamentally different way of specifying a dihedral? (2) In that above example from the CHARMM ffbonded.itp, what is the cp column? Table 5.5 of on page 125 of Section 5.7 of the manual seems to say that in type 9, phi_s, k_phi, and the multiplicity are specified. Does this mean that cp corresponds to the force constant k_phi? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- 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] Type 9 dihedral in Gromacs topology
On 2012-10-27 01:20:15PM -0400, Andrew DeYoung wrote: (1) What is a type 9 dihedral? On page 74 of Section 4.2.12 of the manual, it says, For certain force fields, type 9 is useful. Type 9 allows multiple potential functions to be applied automatically to a single dihedral in the [ dihedral ] section when multiple parameters are defined for the same atomtypes in the [ dihedraltypes ] section. What does this mean? What does it mean to apply multiple potential functions to a single dihedral? Is this a fundamentally different way of specifying a dihedral? It means what it says. Look at the charmm's ffbonded.itp file closely again, in the dihedral section. You will see that for each combination of dihedral angles, you can have multiple potentials defined with different multiplicities. In a non-type 9 dihedral potential gromacs would complain about a second dihedral definition for the same dihedral and override the first. Example: CE2 CE1 CT2 CT3 9 180.00 2.092 1 CE2 CE1 CT2 CT3 9 180.00 5.4392 3 (2) In that above example from the CHARMM ffbonded.itp, what is the cp column? Table 5.5 of on page 125 of Section 5.7 of the manual seems to say that in type 9, phi_s, k_phi, and the multiplicity are specified. Does this mean that cp corresponds to the force constant k_phi? Yes, although the CHARMM people call it KChi. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] About Solvation of Lipid Protein
On 10/27/12 5:16 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply I am following your Protein-lipid Tutorial ( KALP peptide in DPPC) In your tutorial How many Number of Water Molecules you needed to solvate Lipid -protein When I solvate The Number of Water Molecules are 57647 Is it Too high Or Ok If you are working with the tutorial system, that's too many water molecules. I can't remember the exact number, but I'm sure it's lower. If you're working with your own system, I'm not going to try to blindly guess at what might be correct. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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
