[gmx-users] Fwd: RMSD calculation of a specific region

I want to calculate the rmsd of amino acid 65 to 67 of two simulated proteins with loop replacement in another one to find out how the position of these 3 amino acids change due to the replacement of a loop region in same protein ... How can I achieve it with gromacs... -- Bharat Ph.D. Candidat

[gmx-users] fatal error

Dear users, Gromacs 4.5.3 pdb2gmx -f xxx.pdb -water spc select Force Field:9 *Fatal error:* atom C not found in buiding block 13NH2 while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors How c

[gmx-users] charge group radii larger that rlist-rvdw

Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: -- --- ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10 10 ; FREQ

[gmx-users] Error in generating DPPC using grompp

dear all, i am new to gromacs and i'm trying to run the command grompp -c lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr. however i got this error Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp ERROR 1 [file ffgmxbon_lipid.itp, line 756]:

Re: [gmx-users] Fwd: RMSD calculation of a specific region

bharat gupta wrote: I want to calculate the rmsd of amino acid 65 to 67 of two simulated proteins with loop replacement in another one to find out how the position of these 3 amino acids change due to the replacement of a loop region in same protein ... How can I achieve it with gromacs.

Re: [gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did

Dear All Can someone please tell me how to generated the plot of mean force having ran the pull code at several distances using constraints? Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.groma

[gmx-users] Pull code

Dear All Sorry wrong subject title in previous post. Can someone please tell me how to generated the plot of mean force having ran the pull code at several distances using constraints? Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: - ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10

Re: [gmx-users] fatal error

ahmet yıldırım wrote: Dear users, Gromacs 4.5.3 pdb2gmx -f xxx.pdb -water spc select Force Field:9 *Fatal error:* atom C not found in buiding block 13NH2 while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Do

Re: [gmx-users] Error in generating DPPC using grompp

shobana visolingam wrote: dear all, i am new to gromacs and i'm trying to run the command grompp -c lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr. however i got this error *Opening library

Re: [gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did

Gavin Melaugh wrote: Dear All Can someone please tell me how to generated the plot of mean force having ran the pull code at several distances using constraints? Would the mean force not simply be the average value found in pullf.xvg? -Justin Gavin -- ==

[gmx-users] DSPC all atom .itp file

Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

[gmx-users] OPLS implicit solvent problems

Hello, I try to perform an implicit solvent simulation with Gromacs 4.5.3. version. I have a system corresponding to 6 peptides generated by Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA and i put the N-and C- termini as NH2 and COOH. My topology file is correc

Re: [gmx-users] OPLS implicit solvent problems

Hi! Thanks for pointing this out. It is unfortunate that they are missing from the gbsa.itp-file. I will add them, but I do not have time today. If you want to get going, you can add them yourself. The gb-parameters are essentially based on atom hybridization, so for each missing atom you find

[gmx-users] (no subject)

Hi Pers, thank you for reply. I'm trying to add these missing atoms with your guideline, but I don't know if all parameters that I'm going to add are corrects. When you have a time, can you add these missing atoms in the program or can you help me to create a correct substitution of

[gmx-users] CG to FG transformation error

Hi, I am trying to convert a coarse grained protein to a full atom model after CGMD. I am using the modified gromacs_reverse code available from MARTINI site. I am using the following command: g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro But in the output full.gro all

Re: [gmx-users] Problem with using topolbuild1_3.tgz

On Thu, January 20, 2011 at 6:41PM, Sweta Iyer wrote: > Hi, I am trying to generate topology files for a set of lipids with the > help of topolbuild1_3.tgz package found at the other software page of > GROMACS website. > > I downloaded and installed all files and tried running the program with a

Re: [gmx-users] CG to FG transformation error

On 21 Jan 2011, at 14:47, Anirban Ghosh wrote: I am trying to convert a coarse grained protein to a full atom model after CGMD. I am using the modified gromacs_reverse code available from MARTINI site. I am using the following command: g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg

Re: [gmx-users] charge group radii larger that rlist-rvdw

Sir, What exactly can be wrong with the topology? As I tried with different PDBs of same structure at higher resolutions too, I am getting almost similar charge group radii, so can you kindly elaborate about what can go wrong in the topology to get such values? Thanks MKS On Fri, Jan 21, 2011

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Sir, What exactly can be wrong with the topology? As I tried with I don't know, what's in your system? Was the topology created entirely by pdb2gmx, or have you introduced some other molecules that you've parameterized? different PDBs of same structure at higher r

[gmx-users] RNA with small molecule

Hi all, I am trying to simulate RNA with a small molecule. However, I could not find any parameter file described for RNA and small molecule. If anyone knows and shares with me, it is appreciated. Thanks a lot Muslum -- Muslum ILGU PhD Candidate, Nilsen-Hamilton Laboratory Department of Biochemi

Re: [gmx-users] RNA with small molecule

Muslum Ilgu wrote: Hi all, I am trying to simulate RNA with a small molecule. However, I could not find any parameter file described for RNA and small molecule. If anyone knows and shares with me, it is appreciated. You haven't said what force field you'd like to use, which is an importa

Re: [gmx-users] RNA with small molecule

Hi again, I am sorry I fotgot to mention that I will simulate a drug (an antibiotic) with 23mer RNA molecule. I am potentially using GROMOS as a force field to. Thanks On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul wrote: > > > Muslum Ilgu wrote: > >> Hi all, >> >> I am trying to simulate RN

Re: [gmx-users] RNA with small molecule

Muslum Ilgu wrote: Hi again, I am sorry I fotgot to mention that I will simulate a drug (an antibiotic) with 23mer RNA molecule. I am potentially using GROMOS as a force field to. GROMOS is a relatively poor choice for simulations involving nucleic acids. CHARMM or AMBER would be a bette

Re: [gmx-users] fatal error

I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as far as I understand from mailing list. I am using 43a1 forcefield. I do not understand what kind of changes should I do. *the aminoacids.rtp file:* [ ACE ] [ atoms ] CA CH3 0.000 0 C C 0.380 1

Re: [gmx-users] fatal error

ahmet yıldırım wrote: I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as far as I understand from mailing list. I am using 43a1 forcefield. I do not understand what kind of changes should I do. You do not need to modify the .rtp file, you need to modify your coordina

Re: [gmx-users] fatal error

Dear justin, I looked at the pdb file. No NH2 reside contains carbon atom. What should I do? 22 Ocak 2011 00:18 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as >> far as I understand from mailing list.

Re: [gmx-users] fatal error

ahmet yıldırım wrote: Dear justin, I looked at the pdb file. No NH2 reside contains carbon atom. What should I do? In this case, you need to manually specify termini. Choose "None" to allow your capping groups to be built properly. -Justin 22 Ocak 2011 00:18 tarihinde Justin A. Lemku

Re: [gmx-users] Box size and potential energy calculation

On 21/01/2011 6:47 AM, Christian Mötzing wrote: Hi, I currently read through the GMX manual 4.5.3. I have two questions: 1) Density is calculated by the density of the material and the box volume. But I can't find a reference on how the box size is calculated. Can you point me to some literatur

Re: [gmx-users] Fwd: RMSD calculation of a specific region

On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul wrote: > > > bharat gupta wrote: > >> >> >> I want to calculate the rmsd of amino acid 65 to 67 of two simulated >> proteins with loop replacement in another one to find out how the position >> of these 3 amino acids change due to the replacemen

Re: [gmx-users] Fwd: RMSD calculation of a specific region

bharat gupta wrote: On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul > wrote: bharat gupta wrote: I want to calculate the rmsd of amino acid 65 to 67 of two simulated proteins with loop replacement in another one to find out how the

Re: [gmx-users] charge group radii larger that rlist-rvdw

Sir, System is a protein with 123 aa. No modifications were made on the pdb file, and it was submitted to pdb2gmx by removing all HETATMs, retaining only protein atoms. topology was created entirely by pdb2gmx and no other molecule was introduced. I will go through the OPLSAA paper, but

[gmx-users] DSPC all atom .itp file

Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

[gmx-users] Re: Problem with using topolbuild1_3.tgz

- > >Controlling these atoms they corresponding to: > >opls_912B= the  CA of N-terminal residue > >opls_267= Co in COOH > >opls_268= Oh in COOH > >opls_269= Oc in COOH neutral >

[gmx-users] doubts on g_confrms output

Hi, I was trying to do some analysis following John's "GROMACS tutorial for solvation study of spider toxin peptide". I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was g

Re: [gmx-users] doubts on g_confrms output

Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, "Kwee Hong" wrote: Hi, I was trying to do some analysis following John's "GROMACS tutorial for solvation study of spider toxin peptide". I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1