[gmx-users] (no subject)

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[gmx-users] Manual Counterion Placement

Hello, I would like to manually place a counterion into my system with the genion command for which I am pretty sure I will need an index file. My question is how to properly select the specific water atoms / or SOL residue(?) number (that I get from my pdb or gro file) so that it

[gmx-users] tpbconv question

Hello, I'm trying to turn off a Na+ charge using tpbconv in 4.5.4. There is only one Na+ counterion in my simulation. I create an index file, run tpbconv, and my output file looks like the following: [mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq

[gmx-users] Hydroxide Ion

guidance anyone could provide would be very much appreciated. I have tried searching the archives but didn't find anything. Thanks Marc Charendoff ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Zn parameterization

Hello, I am curious - is there anyway to see what assumptions were made when parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally coordinated? With waters only or with imidazoles? Do the different force fields make different assumptions? Guidance appreciated. Regards, Mar

[gmx-users] (no subject)

So sorry! You're absolutely right. Re the question on Zn 2+ I am asking about the ffgmx forcefield. Marc Charendoff wrote: > Hello, > >        I am curious - is there anyway to see what assumptions were made when >parameterizing the Zn 2+ ion? Was it tetrahedrall

[gmx-users] FF 43a1 - Residue Name / Editor Prob?

Hey all, I am trying to pdb2gmx a pdb file using the 43a1 force field and despite my checking the .atp and .rtp files, I still get the following error . . . Back Off! I just backed up posre_A.itp to ./#posre_A.itp.2# Processing chain 2 '+' (2 atoms, 1 residues) There are 0 donors and 0 acce

[gmx-users] Both atom and residue type four letters . . .

Hello,   Well, I have tried a couple of permuatations and I seem to clear up one problem only to get another. Any hints as to what to do when both atomtype AND residuetype each are four letter designates? Not seeing anything in the manual.   Thanks again.     Back Off! I just backed up posre_A.it

[gmx-users] Strange MPI problems. . .

Hello, I am trying to perform a position restrained MD run on our school cluster on a system I have successfully run on before. The only difference is that this new run uses the 43a1 force field (the original used gmx). All my preprocessing has gone well, but when I submit to the cluste

[gmx-users] Hydroxide Attempt

Hello,     I am attempting to see if I can process and run a hydroxide ion using  the ffG43a1 force field. In doing this  I have read through chapter 5 of the manual and have a couple of questions. I do realize that the chemistry and physics of this will need to be justified, but at this point

[gmx-users] Control Atoms for Hydroxide ?

Sorry for bringing up the hydroxide ion question again, but are there any hints as to how to place a single hydrogen on the oxygen atom? Can I somehow assign control atoms outside the hydroxide anion as a means of reference for the required ffG43a1.hdb modification? Looks like both methods to a

[gmx-users] LIE precision and accuracy

Hello,   I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and each solvated ligand through a 1 ns MD simulati

[gmx-users] g_energy question

I am looking at the pairings for a given g-energy and see terms like: LJ-SR:C6Lrest LJ-LR:C6Lrest LJ-14:C6L-rest I know LJ, and SR, LR, 14. C6L is a ligand I am studying.What is a C6L-"rest" interaction? Guidance appreciated. Thanks, Marc-- gmx-users mailing listgmx-users@groma

[gmx-users] Coulomb LR - PME vs. Cut-off

Hello, I am currently running MD on a protein-ligand complex centered in an (approx) 70.0 Angstrom ^3 water box with sodium counterions. I have run  1.0 ns simulations under two different conditions. The first condition with coulombtype "cut-off" I have run to perform LIE calcs as I have r

[gmx-users] g_dist error?

Hello, I am in the middle of analyzing the distance between two atoms of a MD trajectory when I ran into the following error thus stopping at 3 ns of a 4 ns trajectory. What could be the issue? Select a group: 18 Selected 18: 'a_1899' Select a group: 19 Selected 19: 'a_2498' trn version:

[gmx-users] g_cluster settings

Hello, I am trying to perform a cluster analysis on a 4 ns trajectory (4000 frame trajectory), but I am not getting any more than 1 cluster until I get down to a cutoff of 0.05 nm. This seems like an awfully small number, so I checked my rmsd distribution and found that 44% of my rmsds ar

[gmx-users] g_cluster Jarvis-Patrick

Hello, In the Jarvis-Patrick method g_cluster shows that when M=0, the cutoff is used to determine nearest neighbors (those within X.X nm). In the absence of cutoff - e.g. M is defaulted to 10, how are nearest neighbors determined? What does M=10 (or anyother number) mean? Thanks, Marc--

[gmx-users] A Better Question - OS X Config

Sorry all, Here is a better question having read the on-line manual. How do I modify the following BASH config files so I can gmx commands understood. (e.g. pass the "luck" command test). What is my if I'm running an intel iMAc OS 10.4? Guidance appreciated. **computer-2:/etc root# cat p

[gmx-users] grompp problem - usr archives searched

Hey all, First, let me say that I have searched the archives and followed the advice given to check all file and folder write permissions as per M. Abraham. . . Never the less, I'm trying to run grompp, but upon execution I get the following error: creating statusfile for 1 node...

[gmx-users] What is this??

I've been trying to follow the Enzyme-drug tutorial by Kerrigan when I ran into the following: My input as per tutorial. . . . 2:/gromacs Marc$ genbox -cp trp2.pdb -cs spc216.gro -o trp_b4ion.pdb -p trp.top Here is the output . . . . Opening library file /gromacs/share/gromacs/top/aminoacids.

[gmx-users] Attempting small molecule . . .

Hey All, I'm in the middle of trying to perform a MD sim on a homoserine lactone. I built the molecule and ran it through the PRODRG server and retrieved the .gro and .itp files for processing. I call grompp as such: grompp -f minim.mdp -c AHLFIN.GRO -p topol.top -o input.tpr It returns the foll

[gmx-users] More on small molecule attempt...

Hey all, I have learned to match up .itp file atom types to the proper force field when constructing a .gro, .top pair for grompp. However, I have now encountered another stopping point. For given input: grompp -f minim.mdp -c AHLFIN.GRO -p topol.top -o input.tpr I now get . . Back Off! I just

[gmx-users] Sorry, More on small molecule attempt...

Hey All, Also, what is the correct way to coordinate results from make_ndx and the *.mdp variables "energygrps" and "xtc_grps" to ensure grompp can reconcile between the two? Thanks for your patience. --- Marc Charendoff <[EMAIL PROTECTED]> wrote: > Date: W

[gmx-users] Sigh . . . Protonating PDB for PRODRG

Hey all, I'm trying to import energy minimization files into VMD to view and I'm getting some errors. First I note that: • small molecule pdb file shows a total of 48 atoms • my new molecule topology (*.itp file, and *.gro file) show 22 atoms, which I thought were non

[gmx-users] Topology Manipulation question

Hello, I'm running grompp on two small molecules in a single .gro file using the following topology file: #include "ffgmx.itp" #include "BDEX.ITP" #include "AHL.ITP" #include "spc.itp" [ system ] BDEX AHL [ molecules ] BDEX 1 AHL 1 Part of my output looks like the following: Back O

[gmx-users] Thanks to Giovanna! Now, exploding system . . .

With Giovanna's help I was able to complete a grompp run on my system. I did, however get a warning: WARNING 1 [file "topol.top", line 12]: Bad box in file Complex.GRO Generated a cubic box 20.000 x1.445 x1.830 What does this mean? Line 12 refers to one of my complex molecules under t

[gmx-users] This may be it, but what to do?

Here's what I've been able to do so far . . . 1. Generated a two molecule complex and saved as .pdb 2. Parsed the file out to retain relative coordinates of each molecule in separate .pdb files 3. Run both resulting molecules through PRODRG server to generate .gro files for GMX processing. 4.

[gmx-users] Box vector question

Hey all. I'm trying to visualize a *.gro file w/VMD and am having no luck. VMD developer says: Hi, Here's the only .gro file format spec I can find presently: http://www.gromacs.org/documentation/reference/online/gro.html My understanding of that specification is that while the last 6 of the 9

[gmx-users] Text Editor Got Me. . .

Hey All, After wrestling with the *.gro file end-of-file issue I though about the situation... 1. Some files I appended arbitrary box vectors to revealed structures in VMD that looked "smeared." 2. Some .gro files I couldn't view regardless of the box vectors I inserted. 3. GROMACs exploded on

[gmx-users] Partial Charges PM3 ?

Hey all,       I would appreciate an opinion on this. Is it acceptable to caluclate partial charges using a semi-empirical method (PM3) for topologies obtained frmo PRODRG? Is there any vital information that gets missed or skewed by doing this?  I have noticed that some QM/MM strategies will use