[gmx-users] (no subject)
http://kriture.com/site/wp-admin/images.php?time157.php -- 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] rotamers and rings
Hello gromacs users, I have asked this question before but perhaps I was not clear enough. I noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the initial structure has some side chains located very close to each other then after energy minimisation they become distorted (for example, Phe ring is not flat, and for Leu some hydrogen atoms move away from the rest of the side chain).I realize that these problems are probably due very close packing of the sidechains in the initial structure. But I hope to keep the close contacts in the initial structure and obtain correct stereochemistry of the molecule after the minimisation. Is this possible? Sorry for bothering you again and thank you in advance for your help,Abdullah Ahmed -- 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] rotamers during minimization
Hello, I would like to know if gromacs is designed to try and keep as close to the original structure as much as possible? After minimizing a structure with phenyl-alanines I realized that a better minimization could be achieved if the rotamer had been changed during the minimization. However I have been unable to induce gromacs to do this on its own during minimization. I could of course, change the original structure but I prefer not to. Thank you in advance, Abdullah Ahmed My .mdp file is as follows: ;; User spoel (236); Wed Nov 3 17:12:44 1993; Input file;;cpp = /usr/bin/cppdefine = -DPOSRES constraints = noneintegrator = steepnsteps = 2000;; Energy minimizing stuff:;emtol = 0.2emstep = 0.001 nstcomm = 1ns_type = gridrlist = 1rcoulomb= 1rvdw= 1Tcoupl = noPcoupl = nogen_vel = no -- 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] Increasing machine precision
Hello, Is there a way to continue minimizing after reaching machine precision? Emtol and the number of iterations are sufficient to continue. I am assuming that reaching machine precision means that the gradient of change from one iteration to another has become so small that further minimization will not improve the structure. Is this correct? If so is it possible to change the cut-off point for this gradient? Thank you in advance, have a nice day, Abdullah -- 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] Minimization and torsion angles
Hello, I have an input structure with poor torsion angles and after minimization with gromacs (both steepest descent and congugate gradient) I found that they were not corrected. There is enough free space for the torsion angles to be corrected. (I am sure of this because when I run the same structure in Insight it is able to correct them. Both programs give very similar structures with the major difference being the torsion angles.) Has this happened because Gromacs potentials do not penalize poor omega angles? Or have I done something wrong? (I have added by .mdp file at the end of the mail) Is there a way besides applying a restraint to every torsion angle to induce Gromacs to correct them? Thank you in advance for you help, Abdullah ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp = /usr/bin/cpp define = -DPOSRES constraints = none integrator = cg nsteps = 2000 ; ;Energy minimizing stuff ; emtol = 2 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no -- 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] minimization quagmire
Hello everyone, I have a question regarding the results of minimization. I have two structures that are the same except for 2 residues in the core of the structure that have been changed from luecine to to glycine. The leucine structure is very well packed and the core is hydrophobic. The introduction of two glycines in the center creates a a cavity in this hydrophobic region. I had expected the leucine structure to have better(lower) energy after optimization, however, the opposite was true. I have run minimization in vacuum and with water (water enters the cavity) and the structure with glycine has better energy in both cases. The minimization procedure is what I think is standard, the em file is as follows: ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp = /usr/bin/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 1000 ; ;Energy minimizing stuff ; emtol = 20 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no I am using gromacs on windows through cygwin. Thank you in advance for your help, Abdullah -- 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] Internal Density
Dear all, I have 2 structures similar to a Beta-turn where the inside is hydrophobic, and I would like to find the density of just this part of the strucuture. More specifically, both structure are identical expect for one mutation. One of the structures contains 2 glycines facing each other and the other contains a glycine facing a tryptophan. I would like to know if there is a functionality in gromacs that can measure the difference of density between the two strucutres. Thank you in advance, Abdullah -- 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] editconf
Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o)Run editconf to define the box (editconf -d 1)run gromp and mdrun for the minimizationRun editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? Thank you in advance, Abdullah -- 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] position restraints
Hi, Sorry to bother you again, but I am new to gromacs and many theings don't make sense yet. I have tried reading the manual but I do not understand what you mean by "Note how the automatically-generated "posre.itp" file is #included at the end of the Protein_A moleculetype, *before* any other molecules are introduced. You have to do the same with any new #include statements or directives you add." I tried using #include in front of my code for [position_restraints] but that just gives an error. So I suppose that isn't what you mean. Furthermore, in section 5.7.1 of the manual pg110 an example topology file called urea.top is shown. there is no include there. In this example .top file they just seem to have added the position restraints they want after the dihedrals. This approach does not seem to be working for me and I can not understand why. Thank you again for your help, Abdullah > Date: Thu, 3 Jun 2010 09:43:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] position restraints > > > > abdullah ahmed wrote: > > Hi! > > > > In your previous mail you mentioned: > > > > The position restraints must belong to the [moleculetype] of > > the species to be restrained. * Once you #include a new molecule, you > > start a new > > [moleculetype] entry and the position restraints belong to it. * > > > > > > So I rechecked my .top file and found that [moleculetype] only occurs > > once. Perhaps I have misunderstood you. So I added the top file below. I > > No it doesn't. Each time you #include a new .itp file, you are telling > grompp > to copy and paste the contents of that .itp file in that location. Have a > look > at spc.itp - it starts a new moleculetype. > > http://www.gromacs.org/Documentation/Include_File_Mechanism > > Note how the automatically-generated "posre.itp" file is #included at the end > of > the Protein_A moleculetype, *before* any other molecules are introduced. You > have to do the same with any new #include statements or directives you add. > > -Justin > > > did not add the contents of [atoms] [bonds] etc because I felt the mail > > would become unnecessarily long. > > > > ; Include forcefield parameters > > #include "ffoplsaa.itp" > > > > [ moleculetype ] > > ; Namenrexcl > > Protein_A 3 > > > > [ atoms ] > > > > [ bonds ] > > > > [ pairs ] > > > > [ angles ] > > > > [ dihedrals ] > > > > [ dihedrals ] > > > > ; Include Position restraint file > > #ifdef POSRES > > #include "posre.itp" > > #endif > > > > ; Include water topology > > #include "spc.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcxfcyfcz > >11 1000 1000 1000 > > #endif > > > > ; Include generic topology for ions > > #include "ions.itp" > > > > [ system ] > > ; Name > > Protein > > > > [ molecules ] > > ; Compound#mols > > Protein_A 1 > > > > Thanks again for your help, > > Abdullah > > > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign > > up now. <https://signup.live.com/signup.aspx?id=60969> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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 _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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
FW: [gmx-users] position restraints
Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I did not add the contents of [atoms] [bonds] etc because I felt the mail would become unnecessarily long. ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] [ bonds ] [ pairs ] [ angles ] [ dihedrals ] [ dihedrals ] ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 Thanks again for your help, Abdullah Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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
FW: [gmx-users] position restraints
Thank you for your reply, I have been using [ position_restraints ], I do not know why it came out that way in the mail. I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thought that was the way it was supposed to be done. Perhaps this is incorrect. The final lines of the .top file are: Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 [ position_restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; > Date: Thu, 3 Jun 2010 09:00:36 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] position restraints > > > > abdullah ahmed wrote: > > Hello, > > > > I would like to restrain my molecule to a specific position in space. I > > would like for certain atoms to lie on the y-axis. To do this I used > > the following code/lines in my .top file: > > > > [ position restraints ] > > This is an incorrect directive. It should be position_restraints. > > > 2 1 1000 0 1000 ; > > 3 1 1000 0 1000 ; > > 4 1 1000 0 1000 ; > > 5 1 1000 0 1000 ; > > 6 1 1000 0 1000 ; > > 7 1 1000 0 1000 ; > > 8 1 1000 0 1000 ; > > 9 1 1000 0 1000 ; > > > > Unfortunately, after minimization my file contained the molecule in the > > same position as when the restraints were not applied. > > > > Does anyone know what I am doing wrong? > > > > Perhaps the directive name is an issue, although I think grompp should have > raised a warning of some sort. Otherwise, is this block within the > appropriate > [moleculetype] in the topology? Is it under control of an #ifdef block that > you > haven't invoked in the .mdp file? > > -Justin > > > Thanks in advance, > > Abdullah > > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > > now. <https://signup.live.com/signup.aspx?id=60969> > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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 Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] position restraints
Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Unfortunately, after minimization my file contained the molecule in the same position as when the restraints were not applied. Does anyone know what I am doing wrong? Thanks in advance, Abdullah _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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] The components on potential energy
Hello, I would like to ask for some information about the potential energy term in the log file after minimization. I have used the OPLS-AA forcefield to conduct minimization. I understand that it is the addition of a group of energy terms (bond energy, angle, LJ ect..) however, I do not know the individual components that make up potential energy term. Thank you in advance, Abdullah _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] electro-static interaction not made
Dear GROMACS users, I have a protein structure with two oppositely charged residues facing each other. They are close enough for an electrostatic interaction to occur between them. However, this does not occur. After minimization they are in the exact same positions as before. Is there some way to confirm that an electrostatic interaction is not being made in the structure with two charged residues facing each other? And if this is the case, do you have any idea as to why this is happening? Perhaps the following information will prove helpful: I have another structure where there is only one charge (GLU) and one uncharged residue in the same positions as the charged residues in the previous structure. The coulomb energy values of the two structures after minimization do not show much difference (-3.9e+04 compared to -4.0e+4, where -4.0e+04 corresponds to the structure with two charges facing each other). Theoretically, this difference should be greater as the unsatisfied single charge is not as stable. To me the similar coloumb energies suggest that the electrostaic interactions are not being made in the structure with two opposite charges. My .mdp file is as follows: ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 1000 ; ;Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no Thank you in advance! Abdullah _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] naive question about the c-terminus
Perhaps I should also add that the N-terminus is working fine. I have two hydrogen molecules bound to the nitrogen on the N-terminus, and Gromacs can read that fine. I can also ask it to make the terminus NH3, and that works fine too. > Date: Mon, 10 May 2010 11:00:06 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from residue number 23, the residue labelled 44 in the PDB is the > > residue that the error message refers to. Actually there is no residue > > 22 in the PDB file. > > > > You are also somewhat correct in saying that there are more than one > > chains. Currectly I am working on one chain, but the original structure > > I was working on had 10 chains (from A -J). This is why it is labelled > > "B". > > > > Then we'll need a lot more information: Gromacs version, your *exact* command > line, and what force field you're using, at least. The .pdb file should work > fine with O1 and O2; the .tdb file should rename them to O and OT, when > adding > the hydrogen (HO), so I don't know why O2 is staying in place when impropers > are > being added. > > -Justin > > > > Date: Mon, 10 May 2010 10:29:18 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] naive question about the c-terminus > > > > > > > > > > > > abdullah ahmed wrote: > > > > Hello everyone! > > > > > > > > I have a naive question and I have been trying to find a solution > > > > myself, but I just don't understand what is wrong. > > > > > > > > When I run pdb2gmx with "-ter" on my molecule I get the following > > error > > > > message when I ask for a COOH to be made at the C terminus (I get no > > > > error when I ask for COO- ): > > > > > > > > Atom O2 not found in residue 22 while adding improper. > > > > > > > > However, My PDB file ends with: > > > > ATOM 282 C LEU B 44 -5.138 -16.681 4.219 1.00 0.00 > > > > B1 C > > > > ATOM 283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00 > > > > B1 O > > > > ATOM 284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00 > > > > B1 O > > > > TER 286 LEU B 44 > > > > > > > > Therefore, the O2 atom is clearly there. > > > > > > > > > > The error message comes from residue 22, not 44. I'm guessing there > > is another > > > chain, for which residue 22 is the C-terminus? Likely this one is > > missing O2. > > > > > > > I considered the idea that the error was because there is no > > Hydrogen at > > > > the end of the PDB file to make the H in COOH. So I used ZZ vega to > > add > > > > a hydrogen to O2. When this did not work I tried adding one to O1, > > but I > > > > kept getting the following error: > > > > "Atom H1 in residue 22 not found in rtp entry with 19 atoms..." > > > > > > > > > > The force field expects that all of the atoms in the residue have > > specific > > > names. Adding a hydrogen should be done automatically, from the .hdb > > and/or > > > .tdb file(s). > > > > > > -Justin > > > > > > > Thank you in advance, > > > > Abdullah > > > > > > > > > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign > > > > up now. <https://signup.live.com/signup.aspx?id=60969> > > > > > > > > > > -- > > > > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > 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 list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please
RE: [gmx-users] naive question about the c-terminus
The gromacs version is 3.3.1, which I am using on cygwin in the windows enviroment. The command I used is: "pdb2gmx -f test.pdb -p test.top -o test.gro -ter" and the forcefield is Encad all- atom forcefield, using scaled down vacuum charges. > Date: Mon, 10 May 2010 11:00:06 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from residue number 23, the residue labelled 44 in the PDB is the > > residue that the error message refers to. Actually there is no residue > > 22 in the PDB file. > > > > You are also somewhat correct in saying that there are more than one > > chains. Currectly I am working on one chain, but the original structure > > I was working on had 10 chains (from A -J). This is why it is labelled > > "B". > > > > Then we'll need a lot more information: Gromacs version, your *exact* command > line, and what force field you're using, at least. The .pdb file should work > fine with O1 and O2; the .tdb file should rename them to O and OT, when > adding > the hydrogen (HO), so I don't know why O2 is staying in place when impropers > are > being added. > > -Justin > > > > Date: Mon, 10 May 2010 10:29:18 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] naive question about the c-terminus > > > > > > > > > > > > abdullah ahmed wrote: > > > > Hello everyone! > > > > > > > > I have a naive question and I have been trying to find a solution > > > > myself, but I just don't understand what is wrong. > > > > > > > > When I run pdb2gmx with "-ter" on my molecule I get the following > > error > > > > message when I ask for a COOH to be made at the C terminus (I get no > > > > error when I ask for COO- ): > > > > > > > > Atom O2 not found in residue 22 while adding improper. > > > > > > > > However, My PDB file ends with: > > > > ATOM 282 C LEU B 44 -5.138 -16.681 4.219 1.00 0.00 > > > > B1 C > > > > ATOM 283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00 > > > > B1 O > > > > ATOM 284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00 > > > > B1 O > > > > TER 286 LEU B 44 > > > > > > > > Therefore, the O2 atom is clearly there. > > > > > > > > > > The error message comes from residue 22, not 44. I'm guessing there > > is another > > > chain, for which residue 22 is the C-terminus? Likely this one is > > missing O2. > > > > > > > I considered the idea that the error was because there is no > > Hydrogen at > > > > the end of the PDB file to make the H in COOH. So I used ZZ vega to > > add > > > > a hydrogen to O2. When this did not work I tried adding one to O1, > > but I > > > > kept getting the following error: > > > > "Atom H1 in residue 22 not found in rtp entry with 19 atoms..." > > > > > > > > > > The force field expects that all of the atoms in the residue have > > specific > > > names. Adding a hydrogen should be done automatically, from the .hdb > > and/or > > > .tdb file(s). > > > > > > -Justin > > > > > > > Thank you in advance, > > > > Abdullah > > > > > > > > > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign > > > > up now. <https://signup.live.com/signup.aspx?id=60969> > > > > > > > > > > -- > > > > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > 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 list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-
RE: [gmx-users] naive question about the c-terminus
I'm sorry I should have been more clear. Because the PDB file starts from residue number 23, the residue labelled 44 in the PDB is the residue that the error message refers to. Actually there is no residue 22 in the PDB file. You are also somewhat correct in saying that there are more than one chains. Currectly I am working on one chain, but the original structure I was working on had 10 chains (from A -J). This is why it is labelled "B". > Date: Mon, 10 May 2010 10:29:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > Hello everyone! > > > > I have a naive question and I have been trying to find a solution > > myself, but I just don't understand what is wrong. > > > > When I run pdb2gmx with "-ter" on my molecule I get the following error > > message when I ask for a COOH to be made at the C terminus (I get no > > error when I ask for COO- ): > > > > Atom O2 not found in residue 22 while adding improper. > > > > However, My PDB file ends with: > > ATOM282 C LEU B 44 -5.138 -16.681 4.219 1.00 0.00 > > B1 C > > ATOM283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00 > > B1 O > > ATOM284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00 > > B1 O > > TER 286 LEU B 44 > > > > Therefore, the O2 atom is clearly there. > > > > The error message comes from residue 22, not 44. I'm guessing there is > another > chain, for which residue 22 is the C-terminus? Likely this one is missing O2. > > > I considered the idea that the error was because there is no Hydrogen at > > the end of the PDB file to make the H in COOH. So I used ZZ vega to add > > a hydrogen to O2. When this did not work I tried adding one to O1, but I > > kept getting the following error: > > "Atom H1 in residue 22 not found in rtp entry with 19 atoms..." > > > > The force field expects that all of the atoms in the residue have specific > names. Adding a hydrogen should be done automatically, from the .hdb and/or > .tdb file(s). > > -Justin > > > Thank you in advance, > > Abdullah > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign > > up now. <https://signup.live.com/signup.aspx?id=60969> > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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 _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] naive question about the c-terminus
Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I get no error when I ask for COO- ): Atom O2 not found in residue 22 while adding improper. However, My PDB file ends with: ATOM282 C LEU B 44 -5.138 -16.681 4.219 1.00 0.00 B1 C ATOM283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00 B1 O ATOM284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00 B1 O TER 286 LEU B 44 Therefore, the O2 atom is clearly there. I considered the idea that the error was because there is no Hydrogen at the end of the PDB file to make the H in COOH. So I used ZZ vega to add a hydrogen to O2. When this did not work I tried adding one to O1, but I kept getting the following error: "Atom H1 in residue 22 not found in rtp entry with 19 atoms..." Thank you in advance, Abdullah _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] distances between atoms in an electrostatic interaction
Dear Gromacs users, I have an electrostatic interaction in my structure between GLU and LYS. After minimization the distance between the Hydrogen molecule on the Lysine and the Oxygen on the GLU is reduced to 1.4 A°. Is it possible to pre-set this distance to be 1.6 A° instead? I realize that using a distance restraint could be one way to do this. I would like to know if there is another way to do it that will not affect the final toa=tal energy term. Thank you in advance, Abdullah _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] electro-static potential energy after minimization
Thank you for your replies. You guys were right about the problem. The effect of the electrostatic interaction was being masked by the contribution of water to the coulombic energy. I wanted to ask if there was some way to run minimization or MD in a vacuum? I only started using GROMACS last week and my understanding is limited at the moment. If I understand correctly to do MD or minimization one has to first run the "pdb2gmx", "editconf", "genbox", and "grompp" before being able to run "mdrun." But doing so forces you to add water at the editconf/genbox stage. Is there another way to do this? Thanks again, and Bonne Journée! Abdullah > Date: Wed, 5 May 2010 01:47:29 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] electro-static potential energy after minimization > > On 5/05/2010 12:27 AM, abdullah ahmed wrote: > > The charged residues are on the inside of the structure, and so are not > > affected by the solvent. There are also no other charged residues in the > > structure. Furthermore, the structure is quite small 22 (residues). So I > > am still tempted to say that the coloumbic energy of the system should > > be affected by these charges. > > Affected? Yes. Significantly affected? Probably not. The magnitude and > variance of the water-water Coulombic interaction can drown it. It's > analogous to the observation that in order to recognise that a single > person is waving at someone else in a busy crowd, you've got to watch > for a while. > > > Regarding MD, the structure I am using is already in an optimal > > position. I am not particularly interested in refining the structure. > > All I really need is the energy value. > > There is no meaningful single energy value. This is not gas-phase > quantum chemistry. You need to sample an ensemble in order to have the > ability to average out the solvent (and solute!) degrees of freedom. See > http://en.wikipedia.org/wiki/Free_energy_perturbation for example. > > Mark > > > > Date: Tue, 4 May 2010 08:53:48 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] electro-static potential energy after > > minimization > > > > > > > > > > > > abdullah ahmed wrote: > > > > Thank you for your reply, > > > > > > > > However, I can not use MD. > > > > I would simply like to ask whether I am correct in assuming that the > > > > minimized energies of the two structures should be very different. > > > > > > > > > > What exactly are you measuring? The Coulombic energy of the system? > > If so, > > > that term is going to be largely controlled by the solvent and thus > > you will see > > > little, if any, difference at all between the two systems. If you're > > measuring > > > the Coulombic energy between two residues, yes, you should see a > > clear difference. > > > > > > I don't understand your argument against MD. To me, restrained > > minimization > > > doesn't tell you much at all. But maybe I don't fully grasp your > > intentions for > > > these calculations. > > > > > > -Justin > > > > > > > > Date: Tue, 4 May 2010 08:41:15 -0400 > > > > > From: jalem...@vt.edu > > > > > To: gmx-users@gromacs.org > > > > > Subject: Re: [gmx-users] electro-static potential energy after > > > > minimization > > > > > > > > > > > > > > > > > > > > abdullah ahmed wrote: > > > > > > Hello everyone, > > > > > > > > > > > > I have two protein structures, and the insides of both are not > > exposed > > > > > > to water. > > > > > > One structure contains two oppositely charges residues (GLU and > > LYS) > > > > > > facing each other. The second structure contains a GLU residue > > only. > > > > > > Upon minimization I had expected the coloumb energies of the first > > > > > > structure to be lower than that of the second. However, this was > > > > not the > > > > > > case, they are both very similar. > > > > > > Does anyone have an idea as to why this has happened? > > > > > > (The only explaination I can come up with is that perhaps the > > > > effe
re: [gmx-users] electro-static potential energy after minimization
The charged residues are on the inside of the structure, and so are not affected by the solvent. There are also no other charged residues in the structure. Furthermore, the structure is quite small 22 (residues). So I am still tempted to say that the coloumbic energy of the system should be affected by these charges. Regarding MD, the structure I am using is already in an optimal position. I am not particularly interested in refining the structure. All I really need is the energy value. > Date: Tue, 4 May 2010 08:53:48 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] electro-static potential energy after minimization > > > > abdullah ahmed wrote: > > Thank you for your reply, > > > > However, I can not use MD. > > I would simply like to ask whether I am correct in assuming that the > > minimized energies of the two structures should be very different. > > > > What exactly are you measuring? The Coulombic energy of the system? If so, > that term is going to be largely controlled by the solvent and thus you will > see > little, if any, difference at all between the two systems. If you're > measuring > the Coulombic energy between two residues, yes, you should see a clear > difference. > > I don't understand your argument against MD. To me, restrained minimization > doesn't tell you much at all. But maybe I don't fully grasp your intentions > for > these calculations. > > -Justin > > > > Date: Tue, 4 May 2010 08:41:15 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] electro-static potential energy after > > minimization > > > > > > > > > > > > abdullah ahmed wrote: > > > > Hello everyone, > > > > > > > > I have two protein structures, and the insides of both are not exposed > > > > to water. > > > > One structure contains two oppositely charges residues (GLU and LYS) > > > > facing each other. The second structure contains a GLU residue only. > > > > Upon minimization I had expected the coloumb energies of the first > > > > structure to be lower than that of the second. However, this was > > not the > > > > case, they are both very similar. > > > > Does anyone have an idea as to why this has happened? > > > > (The only explaination I can come up with is that perhaps the > > effect is > > > > so small that it can not be seen) > > > > > > > > > > We discussed this at length yesterday. By doing a simple energy > > minimization > > > (in which, if I recall, you are applying position restraints), you > > stand to > > > prove very little. By doing MD and obtaining an ensemble of energies, > > you stand > > > a better chance of calculating a relevant energy. > > > > > > > I was not sure if providing PDB and .mdp files would be helpful, but I > > > > can send then in my next mail if neccesary. > > > > > > > > > > The .pdb file is unnecessary. Only post the .mdp file if it has > > changed since > > > the one you posted yesterday. > > > > > > -Justin > > > > > > > Thank you in advance! > > > > Abdullah Ahmed > > > > > > > > > > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > > > > now. <https://signup.live.com/signup.aspx?id=60969> > > > > > > > > > > -- > > > > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > 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 list gmx-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 ht
RE: [gmx-users] electro-static potential energy after minimization
Thank you for your reply, However, I can not use MD. I would simply like to ask whether I am correct in assuming that the minimized energies of the two structures should be very different. > Date: Tue, 4 May 2010 08:41:15 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] electro-static potential energy after minimization > > > > abdullah ahmed wrote: > > Hello everyone, > > > > I have two protein structures, and the insides of both are not exposed > > to water. > > One structure contains two oppositely charges residues (GLU and LYS) > > facing each other. The second structure contains a GLU residue only. > > Upon minimization I had expected the coloumb energies of the first > > structure to be lower than that of the second. However, this was not the > > case, they are both very similar. > > Does anyone have an idea as to why this has happened? > > (The only explaination I can come up with is that perhaps the effect is > > so small that it can not be seen) > > > > We discussed this at length yesterday. By doing a simple energy minimization > (in which, if I recall, you are applying position restraints), you stand to > prove very little. By doing MD and obtaining an ensemble of energies, you > stand > a better chance of calculating a relevant energy. > > > I was not sure if providing PDB and .mdp files would be helpful, but I > > can send then in my next mail if neccesary. > > > > The .pdb file is unnecessary. Only post the .mdp file if it has changed > since > the one you posted yesterday. > > -Justin > > > Thank you in advance! > > Abdullah Ahmed > > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > > now. <https://signup.live.com/signup.aspx?id=60969> > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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 _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] electro-static potential energy after minimization
Hello everyone, I have two protein structures, and the insides of both are not exposed to water. One structure contains two oppositely charges residues (GLU and LYS) facing each other. The second structure contains a GLU residue only. Upon minimization I had expected the coloumb energies of the first structure to be lower than that of the second. However, this was not the case, they are both very similar. Does anyone have an idea as to why this has happened? (The only explaination I can come up with is that perhaps the effect is so small that it can not be seen) I was not sure if providing PDB and .mdp files would be helpful, but I can send then in my next mail if neccesary. Thank you in advance! Abdullah Ahmed _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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] electrostatic interactions
I wish I could use a picture :) Unfortunately, this is not possible since I need the energy value to be able to compare this to other mutations of the same structure and to provide a "measure" of how energetically favourable one is in comparison to the other. And I am using a box of water because I feel that provides a better estimation of natural conditions than a vaccum :) _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] electrostatic interactions
Actually I'd just like to know why both structures have such similar coloumb energy values. If an electro-static interaction is being made in one structure and not in the other then their coloumb energy values should be different too, no? Wouldn't this be visible with simple energy minimisation? I would prefer to not do molecular dynamics, because the structure is biologically optimal in this conformation and molecular dynamics may move it too much. _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] electrostatic interactions
Thank you for your reply, Settings: I am using the procedure outline by the "speptide" tutorial (i.e. pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp" file I've used is as follows: ; User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp = /usr/bin/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 20 emstep = 0.01 nstcgsteep = 10 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no coulombtype = PME Force field: Encad all atom force field, using full sovent charges. Local geometry is identical with the exception of the second charged residue, which is replaced by Leucine in one structure. > Date: Mon, 3 May 2010 12:11:12 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] electrostatic interactions > > > > abdullah ahmed wrote: > > Hello everyone, > > > > I have just started using GROMACS, and apolise if my question is naive. > > > > Basically, I'd like to ask if anyone has some suggestions regarding the > > settings I should use for electrostatic interactions? > > > > Well, you haven't shown us what settings you're using or what force field > you're > using, so it's impossible to make any specific recommendation. Your cutoffs > and > type of long-range electrostatics method will be largely dictated by the > force > field you've chosen. The primary literature will tell you a lot. > > > I have two protein molecules similar in everyway except, one has a > > single negative charge inside the molecule, and another has two opposite > > charges facing each other. The opposite charges are close enough to form > > electrostatic interactions, so would expect the coloumb energy for this > > molecule to be less than the other after minimization/molecular > > dynamics. However, the results show that they are almost the same. > > > > It's hard to comment on the accuracy of these results without a lot more > information (see above). Other factors include the local geometry of other > surrounding residues; if the structures are different (even subtly) you > certainly can't make any generalizations. > > -Justin > > > Thank you in advance for your help, > > Abdullah Ahmed > > > > > > Hotmail: Powerful Free email with security by Microsoft. Get it now. > > <https://signup.live.com/signup.aspx?id=60969> > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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 _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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] Unneccessary bonding
They are on the inside of the structure. I don't think it is caused by a water molecule, because I ran editconf and genbox again and got the same result. (I have assumed that water molecules are added to the structure in a random fashion in areas not already occupied by other atoms) If you like I can send you the structures in PDB form. > From: x.peri...@rug.nl > To: jalem...@vt.edu; gmx-users@gromacs.org > Subject: Re: [gmx-users] Unneccessary bonding > Date: Mon, 3 May 2010 18:18:31 +0200 > CC: > > > On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote: > > > > > > > abdullah ahmed wrote: > >> Dear Mr. Periole, > >> The atoms that are getting close are oxygen from a GLU residue and > >> hydrogen from a LYS residue. > > > > I don't see anything wrong with a 1.4-A distance between these > > atoms. Why do you suspect a problem (besides the non-existent bond)? > Agreed! This is fine ... the question is why they go from 3.5 to > 1.4 ... are they > embedded in the protein interior? At the surface of the protein > may be a missing water molecule in between them? > > > > -Justin > > > >> Abdullah > >> > >> From: x.peri...@rug.nl > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] Unneccessary bonding > >> Date: Mon, 3 May 2010 18:00:43 +0200 > >> On May 3, 2010, at 5:52 PM, abdullah ahmed wrote: > >>Thank you very much for your reply, I agree it is probably a > >> visualization of the effect, and that there > >>is no bond. However, the distance between the two atoms > >>participating in this "phantom bond" is 1.4 A°. Isn't that too > >>close? Shouldn't it be considered a clash? 1.4 is short for > >> sure! an H-bond goes down to 1.0 ... and charged ions make > >> (depending on their size) bonds with water oxygen around 2.0 ... If > >> you have two opposite charges in front of each other that might > >> well be happening! What kind of atoms are the ones getting > >> close? Abdullah > >> ---- > >>From: x.peri...@rug.nl <mailto:x.peri...@rug.nl> > >>To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > >>Subject: Re: [gmx-users] Unneccessary bonding > >>Date: Mon, 3 May 2010 17:36:29 +0200 > >>On May 3, 2010, at 5:16 PM, abdullah ahmed wrote: > >>Hello, I am a new user to GROMACS and so this > >> question maybe somewhat > >>naive. My objective is to run a few steps of > >> minimization on a PDB > >>structure and then obtain the energy value. To do so I ran the > >>procedure suggested in the tutorial called "speptide" using > >> the > >>.mdp file provided in this procedure. The > >> structure I am using has two oppositely charged residues > >>facing each other. The initial distance(3.2 A°) is such that > >>ionic interactions should occur between them, thereby > >> creating a > >>low coloumb energy score after minimization/molecular dynamics > >>(check by looking at the log-file). However, a covalent bond > >> is > >>being created between them instead. This should not be > >> happening. What do you mean a covalent bond is being created! > >> This is basically > >>not possible! Would that just be a visualization effect? > >> This could result from > >>the fact that the two atoms > >>get really close to each other and thereby your visualization > >>program thinks it is a covalent > >>bond. > >>Does anyone have any ideas on what may be happening and how I > >>can fix it? If this information is not sufficient, > >> please let me know, and > >>thank you in advance. > >>Abdullah Ahmed > >> > >>Hotmail: Free, trusted and rich email service. Get it now. > >><https://signup.live.com/signup.aspx?id=60969> -- > >> gmx-users mailing listgmx-users@gromacs.org > >><mailto:gmx-users@gromacs.org> > >>http://lists.gromacs.org/mailman/listinfo/gmx-users > >>P
RE: [gmx-users] Unneccessary bonding
Dear Mr. Periole, The atoms that are getting close are oxygen from a GLU residue and hydrogen from a LYS residue. Abdullah From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Unneccessary bonding Date: Mon, 3 May 2010 18:00:43 +0200 On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:Thank you very much for your reply, I agree it is probably a visualization of the effect, and that there is no bond. However, the distance between the two atoms participating in this "phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a clash? 1.4 is short for sure! an H-bond goes down to 1.0 ... and charged ions make (depending on their size) bonds with water oxygen around 2.0 ... If you have two opposite charges in front of each other that might well be happening! What kind of atoms are the ones getting close? Abdullah From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Unneccessary bonding Date: Mon, 3 May 2010 17:36:29 +0200 On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is to run a few steps of minimization on a PDB structure and then obtain the energy value. To do so I ran the procedure suggested in the tutorial called "speptide" using the .mdp file provided in this procedure. The structure I am using has two oppositely charged residues facing each other. The initial distance(3.2 A°) is such that ionic interactions should occur between them, thereby creating a low coloumb energy score after minimization/molecular dynamics (check by looking at the log-file). However, a covalent bond is being created between them instead. This should not be happening. What do you mean a covalent bond is being created! This is basically not possible! Would that just be a visualization effect? This could result from the fact that the two atomsget really close to each other and thereby your visualization program thinks it is a covalentbond. Does anyone have any ideas on what may be happening and how I can fix it? If this information is not sufficient, please let me know, and thank you in advance. Abdullah Ahmed Hotmail: Free, trusted and rich email service. Get it now. -- 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 Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. -- 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 _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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] electrostatic interactions
Hello everyone, I have just started using GROMACS, and apolise if my question is naive. Basically, I'd like to ask if anyone has some suggestions regarding the settings I should use for electrostatic interactions? I have two protein molecules similar in everyway except, one has a single negative charge inside the molecule, and another has two opposite charges facing each other. The opposite charges are close enough to form electrostatic interactions, so would expect the coloumb energy for this molecule to be less than the other after minimization/molecular dynamics. However, the results show that they are almost the same. Thank you in advance for your help, Abdullah Ahmed _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] Unneccessary bonding
Thank you very much for your reply, I agree it is probably a visualization of the effect, and that there is no bond. However, the distance between the two atoms participating in this "phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a clash? Abdullah From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Unneccessary bonding Date: Mon, 3 May 2010 17:36:29 +0200 On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is to run a few steps of minimization on a PDB structure and then obtain the energy value. To do so I ran the procedure suggested in the tutorial called "speptide" using the .mdp file provided in this procedure. The structure I am using has two oppositely charged residues facing each other. The initial distance(3.2 A°) is such that ionic interactions should occur between them, thereby creating a low coloumb energy score after minimization/molecular dynamics (check by looking at the log-file). However, a covalent bond is being created between them instead. This should not be happening. What do you mean a covalent bond is being created! This is basically not possible! Would that just be a visualization effect? This could result from the fact that the two atomsget really close to each other and thereby your visualization program thinks it is a covalentbond. Does anyone have any ideas on what may be happening and how I can fix it? If this information is not sufficient, please let me know, and thank you in advance. Abdullah Ahmed Hotmail: Free, trusted and rich email service. Get it now. -- 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 _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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] Unneccessary bonding
Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is to run a few steps of minimization on a PDB structure and then obtain the energy value. To do so I ran the procedure suggested in the tutorial called "speptide" using the .mdp file provided in this procedure. The structure I am using has two oppositely charged residues facing each other. The initial distance(3.2 A°) is such that ionic interactions should occur between them, thereby creating a low coloumb energy score after minimization/molecular dynamics (check by looking at the log-file). However, a covalent bond is being created between them instead. This should not be happening. Does anyone have any ideas on what may be happening and how I can fix it? If this information is not sufficient, please let me know, and thank you in advance. Abdullah Ahmed _ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969-- 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
