[gmx-users] pdb2gmx -missing

I do command pdb2gmx but follow warning and error is came up: WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) Fatal error: There were 1 missing atoms in molecu

[gmx-users] energy minimization - not converge

Hi I want to do energy minimization but follow subject is came up: writing lowest energy coordinates. Back Off! I just backed up ooo.gro to ./#ooo.gro.5# Steepest Descents did not converge to Fmax < 2000 in 101 steps. Potential Energy = -3.2421097e+05 Maximum force = 1.4766100e+04 on atom

Re: [gmx-users] pdb2gmx -missing

Hi, Try to use -ignh. On Wed, Nov 11, 2009 at 7:09 PM, leila karami wrote: > I do command pdb2gmx but follow warning and error is came up: > > WARNING: atom H is missing in residue GLY 1 in the pdb file > You might need to add atom H to the hydrogen database of residue > GLY >

Re: [gmx-users] energy minimization - not converge

Hi Leila, Where does it say that you encountered an error? You also could've checked the wiki/mailing lists for this and found that this is normal and sufficient for starting an MD simulation. Cheers, Tsjerk On Wed, Nov 11, 2009 at 9:10 AM, leila karami wrote: > Hi > > I want to do energy mini

Re: [gmx-users] pdb2gmx -missing

Hi, Well, -ignh is not the right answer here. I recall that just a few days ago someone posted the same problem. For Amber you need to tag the first and last residue. For your GLY, it means you have to rename it to NGLY. Itamar, The warning mentions an atom missing from the .pdb file. These have

Re: [gmx-users] energy minimization - not converge

leila karami wrote: Hi I want to do energy minimization but follow subject is came up: writing lowest energy coordinates. Back Off! I just backed up ooo.gro to ./#ooo.gro.5# Steepest Descents did not converge to Fmax < 2000 in 101 steps. Potential Energy = -3.2421097e+05 Maximum force =

Re: [gmx-users] pdb2gmx -missing

Sorry if I made someone more confuse, I thought this was the problem. Probably reading the original post again would have a wise step. Itamar On Wed, Nov 11, 2009 at 7:25 PM, Tsjerk Wassenaar wrote: > Hi, > > Well, -ignh is not the right answer here. I recall that just a few > days ago someone p

Re: [gmx-users] Does Gromacs support CHARMM force field now?

xuji wrote: Hi all GMX users: I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? No. It will be supported as of version 4.1, as has been stated many

[gmx-users] RE: Does Gromacs support CHARMM force field now?

Hi, I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? The files are there unofficially (that's why they're not included in the ff.dat file) and in an

[gmx-users] Increase temperature to 550K

Hi The system = one lysozyme + TIP3P water I was put the system in NTP simulation. Under 550K, all water molecules should evaporate entirely , I suppose ??? >From Justin => "There are plenty of other methodological concerns (pressure coupling especially) " Would you please direct me about this ?

Re: [gmx-users] Increase temperature to 550K

Chih-Ying Lin wrote: Hi The system = one lysozyme + TIP3P water I was put the system in NTP simulation. Under 550K, all water molecules should evaporate entirely , I suppose ??? Is this what you want to happen? Are the force field parameters appropriate for such behavior? From Justin

[gmx-users] Increase temperature to 550K => simulation techniques ?

Hi For running simulaion parameters, people normally not write the details in their papers. high-temperature (up to 600 K) simulations of proteins in TIP3P.. any other detailed suggestion about this ? Thank you Lin I agree with Mark's earlier comment; the water model alone is not the

[gmx-users] Constraints & Restraints

Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose o

Re: [gmx-users] Constraints & Restraints

darre...@ece.ubc.ca wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a li

Re: [gmx-users] Constraints & Restraints

Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like res

Re: [gmx-users] RE: Does Gromacs support CHARMM force field now?

Pär Bjelkmar wrote: Hi, I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? The files are there unofficially (that's why they're not included in the ff.

[gmx-users] force field: heme group

Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in

Re: [gmx-users] force field: heme group

No, you're wrong. There are parameters for HEME in several flavours of the GROMOS forcefields, which you can find in the share/gromacs/top/ directory. Ramachandran G skrev: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force

Re: [gmx-users] Increase temperature to 550K => simulation techniques ?

Chih-Ying Lin wrote: Hi For running simulaion parameters, people normally not write the details in their papers. That's not normally true - the point of a methods section in a paper is that an experienced practitioner in the field could reproduce the work. That is normally much less detailed

Re: [gmx-users] force field: heme group

Ramachandran G wrote: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, That's not true; all of the Gromos variants have heme parameters. AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my

Re: [gmx-users] force field: heme group

Ramachndran, If you are trying to use the AMBER force field ports for Gromacs (assuming you installed them correctly), I have defined the HEME group for Amber03. If this would help you let me know, and i can provide the files that you need to replace in your gromacs "top" folder -Matt Dani

Re: [gmx-users] force field: heme group

Matthew L. Danielson wrote: Ramachndran, If you are trying to use the AMBER force field ports for Gromacs (assuming you installed them correctly), I have defined the HEME group for Amber03. If this would help you let me know, and i can provide the files that you need to replace in your gr

[gmx-users] Constraints & Restraints

Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, correct? Thanks. Darrell

[gmx-users] Docking with PyMol and using Gromacs

Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open

[gmx-users] Adsorption energy of a single molecule

Hi Justin, So when I create the index file with the molecule and the graphene sheet and run g_energy, is the adsorption energy between the adsorbed molecule and the graphene sheet the LJ (SR) energy? And will this energy be just the interaction energy between the adsorbed molecule and the graph

Re: [gmx-users] Docking with PyMol and using Gromacs

Gunnar Widtfeldt Reginsson wrote: Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organi

Re: [gmx-users] Adsorption energy of a single molecule

Darrell Koskinen wrote: Hi Justin, So when I create the index file with the molecule and the graphene sheet and run g_energy, is the adsorption energy between the adsorbed molecule and the graphene sheet the LJ (SR) energy? And will this energy be just the interaction energy between the adso

Re: [gmx-users] Constraints & Restraints

Darrell Koskinen wrote: Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, co

RE: [gmx-users] Docking with PyMol and using Gromacs

Coordinate files like pdb and gro aren't used by GROMACS to provide any bonding information. That is what the topology files are for. So their "presence" in your pdb isn't an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance betwee

Re: [gmx-users] Docking with PyMol and using Gromacs

Justin A. Lemkul wrote: Gunnar Widtfeldt Reginsson wrote: Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as on

Re: [gmx-users] Adsorption energy of a single molecule

Darrell Koskinen wrote: Hi Justin, So when I create the index file with the molecule and the graphene sheet and run g_energy, is the adsorption energy between the adsorbed molecule and the graphene sheet the LJ (SR) energy? Not necessarily, unless the force field was parameterized to produce