Re: [gmx-users] Free energy of protonation

My advise is a bit general. Try the same process with a different molecule (one that can support this change), try the same molecule with an AA ff, since it is already done (as you mentioned) do you get similar results? These tests might help you find out if there is something wrong with your

Re: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4?

In most cases this means that the exact same line is given more than once. I would start from there. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Adarsh V. K. Sent: Monday, March 9, 2020 1:26 PM To:

Re: [gmx-users] how can I obtain the potential energy of each atom？

Did you try a script that calls gmx energy in each iteration, parsing the index of each atom as an input??? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of zk_dlut Sent: Monday, April 22, 2019 10:49:25 AM To: gmx-us...@gromacs.org

Re: [gmx-users] Trouble with gmx distance

ur index.ndx for better investigation. On Monday, August 21, 2017, 9:24:35 PM GMT+3, Sotirios Dionysios I. Papadatos <si.papada...@edu.cut.ac.cy> wrote: Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx di

[gmx-users] Trouble with gmx distance

Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg" I get the obvious: "Selection 'atom_name' does not evaluate into an even number of positions

Re: [gmx-users] Get a correct .pdb for a synthetic peptide

Hi, to get things straight did you use pdb2gmx or just editconf? Where does the error occur? My personal choice is Maestro which is free for academic use. The resulting pdbs' have no problem with Gromacs. If you want to make minor changes, for example change LIG to DRG (assuming DRG is

Re: [gmx-users] NVT error

Sorry for being late and I hope you already found it yourself, but in any case here goes, in tc-grps you use one system HEM, while right below you enter params for two tau-t = 0.1(1) 0.2(2). Although I don't know what you want to simulate but in general you use: Protein(protein + ligands)

Re: [gmx-users] Propylene Carbonate

automated builders usually produce these mistakes. I see that you already checked which atoms correspond to this error. Check first if there is an actual bond there. If it is check ffbonded if these atom types are parametrized. From:

Re: [gmx-users] Topology error

Furthermore external servers fail to parameterize Fe, so it is of no use anyway. You should find the missing parameters in the literature. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of

Re: [gmx-users] Gro file does not match topology

OK, dividing the number by 3 could be used if you are using a 3-point water solvent. Apart from that, assuming that during the procedure up to minimization you didn't forget to update your topology file, this usually comes up if you manually edit your .gro, .top files. Check your .gro file, top

Re: [gmx-users] European Hardware Vendors

Hi and sorry for being late. My suggestion is a bit off, but wouldn't it be better/easier to work in an existent HPC center? More efficient and less hustle setting up the system. The one my research group uses is: http://web.cytera.cyi.ac.cy/about/ Hope this helps

Re: [gmx-users] converting pdb file to gromacs input file

In pdb2gmx you give as an input the filename.pdb. This should do the trick. But I think there is something else that you truly need. Maybe you need some more info on how to add a hetatm in an existing force field.? From:

Re: [gmx-users] pdb2gmx vsites error reading atom name

Maybe you are trying to simulate a molecule that is not mentioned in the aminoacids.rtp on the force field of your choice or more probably the atom that is mentioned on the error report has a different name than the the one provided on the pdb file. My advice is to check on the ff directory >

Re: [gmx-users] desmond setup

Hi, even if this is not the place for Desmond, your institute has most probably provided you with an email. You can register on their website and download the software for free using an academic (free) license. From:

Re: [gmx-users] Carbon double bond in Gromos

For this I would suggest the following. From your structure remove any ligands and then run pdb2gmx. Open the parameter file and the original file with a visualization tool. Find a carbon from any aminoacid that has a double bond. Check for its name in the force field directory, there you will

Re: [gmx-users] g_membed failure

Hi, run some diagnostics, don't use the -xyinit etc Try the basics gmx g_membed -f -p ... etc Also the way this worked for me was to use an index file. I made an index of the prot + lig + crystallographic waters and I used it in both grompp and g_membed. In the latter I just used the group

Re: [gmx-users] high pressure and temperatures: force field parameters

eers Mohsen On Thu, Sep 8, 2016 at 10:42 AM, Sotirios Dionysios I. Papadatos < si.papada...@edu.cut.ac.cy> wrote: > I am not aware on your question per se, but just to give you food for > thought. Force fields are not based on real values of let's say force > constants.

Re: [gmx-users] high pressure and temperatures: force field parameters

I am not aware on your question per se, but just to give you food for thought. Force fields are not based on real values of let's say force constants. You can't produce for example 'plasma' at least with the default ff, if you overheat. So it not a matter of a ff not being accurate for high

Re: [gmx-users] Atom type 'OM' not found

Maybe your residue has an atom name that is not defined as AMBER 03 ff expects it to. Check the f directory to see how TYR has the atom names defined. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] Is charmm GUI ideal for membrane building

I might be wrong here, but energy is supposed to converge. Maybe you want to verify something else? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Tsjerk Wassenaar

Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is working if I use it solo, not with gmx. It's worth a shot. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] topology and coordinate file not matching after grompp

Hi, in general the error is self explanatory. It means that you have set more atoms in the topology file (usually that is the case). I would suggest a simple script in the language that you are most comfortable with, to count the occurrences of a specific element. Hope this helps.

[gmx-users] question on editconf

I am trying to change the orientation of a protein embedded in a protein. I am using the command editconf -rotate. The output is only the protein without the membrane. My question is if there is a way to do a rotation of the protein in regard to the membrane (I am using an index file). Thanks

Re: [gmx-users] Excessive memory usage of mdrun

Hi, though your system is not that small, you shouldn't have any problem running lysozyme tutorial. Although the number of CPU's only affect the ns/day a simulation runs, it is a matter of your HPC system. Did you install gromacs yourself?? From:

Re: [gmx-users] maestro cms file to gromacs

In maestro export project > (save_as) atomName.pdb Just another way to avoid using another program From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Smith, Micholas D.

Re: [gmx-users] mdp file

M To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp file On 9/1/15 12:50 PM, Sotirios Dionysios I. Papadatos wrote: > Hi, > > I am having some trouble defining a proper mdp file for minimization and > production runs. I am aware of the manual's - site's reference to this > matter, it

[gmx-users] mdp file

Hi, I am having some trouble defining a proper mdp file for minimization and production runs. I am aware of the manual's - site's reference to this matter, it is pretty thourough. My question is: How do I know which parameters to use for each simulation? Is there a publication, book etc to

Re: [gmx-users] (no subject)

This is most probably due to some missing atoms. If you are not trying to include exotic atoms, meaning that you have to add them to aminoacids.rtp etc then you need a program like Schrodinger/maestro to manually add the atoms missing, export it to .pdb and try again. Hope that helps

Re: [gmx-users] pdb2gmx error

If I got it right I would suggest this. Try removing parts in your overall structure. For example let's say your system has 3 components water, ATP, TPO. Try removing all but water, try pdb2gmx, all but ATP ( like a sim in vacuo ) try once again pdb2gmx. This will make the troubled part

Re: [gmx-users] problem using grompp

constraint implementations - see the manual section headed constraint algorithms. Mark On Thu, Jun 11, 2015 at 10:39 AM Sotirios Dionysios I. Papadatos si.papada...@edu.cut.ac.cy wrote: Dear community, I am trying to set parameters for a molecule that doesn't exist in gromacs library. I have

[gmx-users] problem using grompp

Dear community, I am trying to set parameters for a molecule that doesn't exist in gromacs library. I have found all the required data from the literature, apart from bond force constant (Kb). There seems to be a way to overcome this but using constraints on all the bonds using the Settle

Re: [gmx-users] Questions about the topology file format

If I am not mistaken, and there is a chance that I am the length and force constant are used with grompp in ffbonded.itp in the force field directory. After the question mark everything else is indeed not read so it is mostly used by the users for clarification. But I believe that in the part

Re: [gmx-users] (no subject)

Hi, I'm not accustomed with coarse grained, but from the little stuff I know on MD in order to keep a box's size constant you have to use an NVT simulation not an NPT. Meaning don't keep pressure constant but rather the volume. Do double check though, I might be wrong.

Re: [gmx-users] Error using grompp - atomtype not found

...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Monday, May 25, 2015 7:34 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error using grompp - atomtype not found On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos

[gmx-users] Error using grompp - atomtype not found

Hi, I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor. When I try to use grompp it says atomtype opls_ not found. I have added all the needed atoms in atomtypes.atp of the ff I

[gmx-users] How to proceed with molecule.itp file

Hi, I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use. My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use

Re: [gmx-users] How to proceed with molecule.itp file

Hi, This indeed begins to clarify things but just to make sure I got it right. I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule. So I use the pdb2gmx to the molecule, I edit the topol.top that is produced