[gmx-users] Could anybody post a sample.mdp for protein-membrane-aqueous simulation ?

Dear GROMACS UsersI'm doing a simulation of a protein-membrane-aqueous system, I'm not very familiar with the .mdp files of this kind, so, could anybody kind enough send me two sample.mdp files for position restraint and molecular dynamic? The membrane type I chosen is DPPC. Thanks in advance!

[gmx-users] error in pdb2gmx step

Dear all,  I faced a problem in the  pdb2gmx step as i got this following error message, "Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013)" As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great

Re: [gmx-users] error in pdb2gmx step

Check you pdb file and see if the chain identifier A occurs at different places in the file. Pdb2gmx expects a chain to be continous, and if it isn't, it gets confused. If you have several chains, rename them accordingly. Cheers /Per Annie Albin wrote: Dear all, I faced a problem in the

Re: [gmx-users] error in pdb2gmx step

Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin < [EMAIL PROTECTED

[gmx-users] Restart without energies

Hello! I've been running a simulation for a few picoseconds when the machine crashed. The I tryied to use tpbconv, but it said that the .edr file is empty and cannot generate the .tpr file. I suppose that it is due to buffering issues that the .edr file was not written and the .trr file was writte

Re: [gmx-users] Restart without energies

Hi Jordi, Now it's too late, but you can always change the mdp option for the frequency of edr writing, nstenergy option. If it's just some ps, maybe it's not really worth doing much about it. Reruning the simulation to get an energy file it's possible with the -rerun option in mdrun, feeding

Re: [gmx-users] error in pdb2gmx step

Well thank you.Yes I did find a region in which chain identifier 'A' was repeating, this corresponded to the HETATM CO, so i tried removing the chain identifier in one case and in another one I tried shifting it to the correspoding chain, but in both cases i got the following error "Fatal error: R

Re: [gmx-users] error in pdb2gmx step

That means that the CO ion type is not described by the forcefield you are using, check the .rtp file of your force field or the ions.itp file in the gromacs/top directory. anyhow be careful not to make any confusion between the chain identifier, which is a 1 character id, and the residue name. Are

[gmx-users] Re: gmx-users Digest, Vol 23, Issue 99

hi all, my gromacs is giving me this LINC ERROR.i found in the mailing list about this and found two suggestion, one to define it as dflexible and another to increase the tau_p to 20(my initial was 0.5).I did increase it step by step in some 20 runs, still the problem persists.the LINC error is

[gmx-users] (no subject)

hi all, my gromacs is giving me this LINC ERROR.i found in the mailing list about this and found two suggestion, one to define it as dflexible and another to increase the tau_p to 20(my initial was 0.5).I did increase it step by step in some 20 runs, still the problem persists.the LINC error is

Re: [gmx-users] Re: Problem with simulated annealing!!!

Dear Bruce, Thank you very much for your suggestion. I tried as you said. But the only difference Which I saw is that the temperautre goes upto 314 (I tried it with 10ps MDrun). After that I tried for 100ps MDrun. I used the same parameters which you have mentioned in the previous mail. I didnt

Re: [gmx-users] Re: Problem with simulated annealing!!!

Hi Poornima,If you can paste the entire mdp file, then it can be easy for the users to suggest you things.Cheers,On 3/31/06, poornima Gajendrarao <[EMAIL PROTECTED]> wrote:Dear Bruce, Thank you very much for your suggestion.I tried as you said. But the only difference Which Isaw is that the temper

[gmx-users] Non-zero system charge

Hello everyone, I am using PME to handle electrostatics. What happens if I run a simulation with a non-zero net charge? Does GROMACS automatically provide some sort of background charge to neutralize the system? Thanks, Bob Johnson ___ gmx-users mailing l

Re: [gmx-users] Non-zero system charge

My understanding is yes. But I think it is still customary to include counterions unless you have some good reason for not doing so. Otherwise, it uses (I think) a uniform background neutralizing charge. On 3/31/06, Bob Johnson <[EMAIL PROTECTED]> wrote: > Hello everyone, > I am using PME to handl

Re: [gmx-users] Non-zero system charge

Shalom Bob, First GROMACS does not nutrelize the charge it will run the system as is, you have to nutrelzie it manually. I know this was discussed few weeks ago, please search the mailiong list. good work, Itamar. Quoting Bob Johnson <[EMAIL PROTECTED]>: > Hello everyone, > I am using PME to

Re: [gmx-users] Non-zero system charge

Itamar, But if the charge weren't neutralized, the electrostatic energy would be infinite, since an infinite lattice of charged unit cells has infinite charge and hence infinite interaction energy. (So the trivial check, of course, is to see whether the energy is infinite if you run with a charge

Re: [gmx-users] Non-zero system charge

David Mobley wrote: Itamar, But if the charge weren't neutralized, the electrostatic energy would be infinite, since an infinite lattice of charged unit cells has infinite charge and hence infinite interaction energy. (So the trivial check, of course, is to see whether the energy is infinite if

Re: [gmx-users] Non-zero system charge

David Mobley wrote: My understanding is yes. But I think it is still customary to include counterions unless you have some good reason for not doing so. Otherwise, it uses (I think) a uniform background neutralizing charge. On 3/31/06, Bob Johnson <[EMAIL PROTECTED]> wrote: Hello everyone, I a

[gmx-users] OPLS-AA angle types !!

Hello all, I am trying to include a new molecule (a long chain lipid) into the oplsaa FF. everything is fine except the angle types and dihedrals. the RB dihedrals were calculated and declared in the ffoplsaabon.itp as described in the manual the angles are given here: CH2OC CH1 11

Re: [gmx-users] OPLS-AA angle types !!

ritwik kavathekar wrote: Hello all, I am trying to include a new molecule (a long chain lipid) into the oplsaa FF. everything is fine except the angle types and dihedrals. the RB dihedrals were calculated and declared in the ffoplsaabon.itp as described in the manual the angles are given here: C

[gmx-users] Facing errors while running grompp

hi guys when i want to solvates the protein transferase (HUMAN PI3KGAMMA COMPLEXED WITH AS605240).that contains hetero atom QYT . i have edited the pdb file and removed the QYT and taken the cordinates from the dundee prodrg server and i got the coordinate files and itp files from that.later i run