Re: [gmx-users] Adding Na ions to DPPG
On Mon, Oct 27, 2008 at 10:21 AM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Peyman Yamin wrote: On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPGx NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. Well this looks great! I simulate one single DPPG in solvent. and you know, this Na+ is not in solvent but a part of DPPG. So you mean I just make a DPPG with an O which has no H so is minus and then use genion to add Na? will it place the Na aroung O hopefully? I think if I put no H arounf O the prodrg will force me to have it! so I should delete it and replace it with Na? or I should never use the word replace at all??? Well, the Na+ may be associated with DPPG electrostatically, but they are still distinct chemical entities. You can have a DPPG that has a net -1 charge; certainly all chemical species are not net neutral! Indeed, genion will place Na+ in whatever solvent you choose, but may not necessarily be bound to DPPG. Some simulation may show the association, however. Yes, keep the DPPG. The charge distribution around anionic lipid has been studied. http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=PRLTAO0001010303810301idtype=cvipsgifs=yes And no, don't replace any part of your DPPG. Because then you don't really have DPPG any more do you? -Justin Thanks again ;) Peyman -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1.I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED] ___ 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 [EMAIL
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. That doesn't make sense to me. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Sodium is not going to form any bond. It's a labile ion, so needs its own [ molecule ] section. The easiest approach is to construct a topology for the anion, and then use genion to add suitable amounts of Na+ afterwards. Check out some tutorial material for the approach here. Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Adding Na ions to DPPG
Use the Gromacs program genion for that purpose. This replaces water molecules by the ions you specify. You may need to change the topology afterwards manually. Make sure, you put an #include ions.ipt near the top of the .top-file, this contains the force field parameters for ions. Best wishes Andreas -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peyman Yamin Sent: 27 October 2008 12:36 To: gmx-users Subject: [gmx-users] Adding Na ions to DPPG Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Thanks a lot for the replies, I replace the O in DPPG because I thought it's practical to get the topology of the quasi-DPPG (which has no charge cause the O is connected to the P) from prodrg, and then delete the O and replace it with Na and delete the bond of P with it and try to tell gromacs it's just a non-bonded Na around the P! since it's always around the P replacing the O which was bond to P made sense to me from the coordinates (distance to P, etc.) point of view. Am I doing strange things?? I'm not sure if I have to use genion since my zwitterionic DPPG has always its Na+ beside its O-. On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. I thought since O on P is gone it will be -1 charged, so a +1 Na will balance it, won't it?? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. Well I do include it. So shouldn't I worry about the nonbonding params and stuff? like those in topology file? Actually an existential question for me always is that if everything goes OK by adding the FF itp, then why does prodrg give me all the params for bonds, dihedrals, angles and etc.?? So, genion or manually replace? and how please...I mean, I don't want to pass my task to others, but well, a bit of more detailed help would enlight me a great deal ;) Cheers, Peyman APPENDIX! * This is the top for the DPPG with the unwanted O --- say O number 24. ** The question is if I simply change that to Na (of course in pdb as well) what changes should I make in other switches? I see non of non-bonding context! (pairs?) [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CBL 1 -0.019 15.0350 2 CH2 1 DRG CBK 10.006 14.0270 3 CH2 1 DRG CBJ 10.006 14.0270 4 CH2 1 DRG CBI 10.007 14.0270 5 CH2 1 DRG CBH 20.000 14.0270 6 CH2 1 DRG CBG 30.000 14.0270 7 CH2 1 DRG CBF 40.000 14.0270 8 CH2 1 DRG CBE 50.000 14.0270 9 CH2 1 DRG CBD 60.000 14.0270 10 CH2 1 DRG CBC 70.000 14.0270 11 CH2 1 DRG CBB 80.000 14.0270 12 CH2 1 DRG CBA 90.000 14.0270 13 CH2 1 DRG CAZ100.039 14.0270 14 CH2 1 DRG CAY100.039 14.0270 15 CH2 1 DRG CAX100.039 14.0270 16 C 1 DRG CAV100.232 12.0110 17 O 1 DRG OAW10 -0.377 15.9994 18OA 1 DRG OAU10 -0.108 15.9994 19 CH1 1 DRG CAT100.136 13.0190 20 CH2 1 DRG CBM110.054 14.0270 21OA 1 DRG OBN11 -0.094 15.9994 22 P 1 DRG PBO110.954 30.9738 23OA 1 DRG OBP11 -0.410 15.9994 24OA 1 DRG OBQ11 -0.410 15.9994 25OA 1 DRG OBR11 -0.094 15.9994 26 CH2 1 DRG CBS120.034 14.0270 27 CH1 1 DRG CBT120.070 13.0190 28OA 1 DRG OBW12 -0.117 15.9994 29 H 1 DRG HCQ120.013 1.0080 30 CH2 1 DRG CBU130.069 14.0270 31OA 1 DRG OBV13 -0.086 15.9994 32
Re: [gmx-users] Adding Na ions to DPPG
On Monday 27 October 2008 14:08, Mark Abraham wrote: Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. That doesn't make sense to me. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Sodium is not going to form any bond. It's a labile ion, so needs its own [ molecule ] section. The easiest approach is to construct a topology for the anion, and then use genion to add suitable amounts of Na+ afterwards. Check out some tutorial material for the approach here. Right, but can't I have them all included in a single top?? What shall I put into the topology of the cation then? I have a single DPPG molecule in water/octanol. So I thought I might just embed the Na inside the DPPG top. in the end DPPG HAS a Na actually, though non-bonded! If I'm way away from making sense then would be happy to know the logical way. about genion I thought it's mainly for adding the ions to the solvent, but I should have exactly one Na. Be well, Peyman Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPGx NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: On Monday 27 October 2008 14:08, Mark Abraham wrote: Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. That doesn't make sense to me. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Sodium is not going to form any bond. It's a labile ion, so needs its own [ molecule ] section. The easiest approach is to construct a topology for the anion, and then use genion to add suitable amounts of Na+ afterwards. Check out some tutorial material for the approach here. Right, but can't I have them all included in a single top?? What shall I put into the topology of the cation then? I have a single DPPG molecule in water/octanol. So I thought I might just embed the Na inside the DPPG top. in the end DPPG HAS a Na actually, though non-bonded! Alright, now I understand. So you will have several different topologies to deal with. You don't need to merge DPPG/Na+ into one! You have separate topologies for water and octanol, too, don't you? You could use the topology from PRODRG as dppg.itp, for example, and construct a .top that has the following: #include ffG43a1.itp #include dppg.itp #include spc.itp #include octanol.itp #include ions.itp [ molecules ] DPPGx SOL y OCT z NA+ 1 All bonded and non-bonded parameters will then be read from the appropriate force field files, without merging anything! -Justin If I'm way away from making sense then would be happy to know the logical way. about genion I thought it's mainly for adding the ions to the solvent, but I should have exactly one Na. Be well, Peyman Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPG x NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. Well this looks great! I simulate one single DPPG in solvent. and you know, this Na+ is not in solvent but a part of DPPG. So you mean I just make a DPPG with an O which has no H so is minus and then use genion to add Na? will it place the Na aroung O hopefully? I think if I put no H arounf O the prodrg will force me to have it! so I should delete it and replace it with Na? or I should never use the word replace at all??? Thanks again ;) Peyman -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPGx NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. Well this looks great! I simulate one single DPPG in solvent. and you know, this Na+ is not in solvent but a part of DPPG. So you mean I just make a DPPG with an O which has no H so is minus and then use genion to add Na? will it place the Na aroung O hopefully? I think if I put no H arounf O the prodrg will force me to have it! so I should delete it and replace it with Na? or I should never use the word replace at all??? Well, the Na+ may be associated with DPPG electrostatically, but they are still distinct chemical entities. You can have a DPPG that has a net -1 charge; certainly all chemical species are not net neutral! Indeed, genion will place Na+ in whatever solvent you choose, but may not necessarily be bound to DPPG. Some simulation may show the association, however. And no, don't replace any part of your DPPG. Because then you don't really have DPPG any more do you? -Justin Thanks again ;) Peyman -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
