[gmx-users] query regarding source of error

I m not getting the meaning of source of error mentioned in user i.e.,charge groups encompass too many atoms. Most charge groups should be less than 4 atoms or less.Let me know the exact meaning of this source of error.Reply me soon. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] query regarding source of error

Hi Anushree, I assume the rudeness of the last two sentences is unintentional. You might benefit from reading http://catb.org/~esr/faqs/smart-questions.html The problem only occurs if you generated a topology by yourself or took it from someone else. That would indicate that you're a relatively

[gmx-users] g_helixorientation question

Hello! My name's Javier Romero and I am a PhD student, writting from Barcelona. I am simulating an anphipatic helix of 23 residues, in the interface of a DPPC membrane and water. I am trying to measure the rotation of the helix using the tool g_helixorientation. Could be somebody so kind to

[gmx-users] maybe you are out of quota?

Dear Gromacs Users, The following error messages appear while running MD simulations with Gromacs 4.5.4: - Cannot flush logfile - maybe you are out of quota? - XTC error - maybe you are out of quota? - Cannot read/write checkpoint; corrupt file, or maybe you are out of quota? - Cannot write

[gmx-users] Topology error

Dear Sir/Madam, For orienting the protein and membrane, I have used the .mdp and following topology file: ; ; File 'topol_popc.top' was generated ; By user: jalemkul (502) ; On host: bevany.biochem.vt.edu ; At date: Fri Oct 20 13:26:53 2006 ; ; This is your topology

[gmx-users] Ligand charge assignment

Dear Sir/madam, I have a ligand molecule for which I generated the topology file using Prodrg software. As the charges and groupings provided by Prodrg are not much reliable. I need to assign correct charges and groupings for my ligand. I had referred the article Practical considerations for

RE: [gmx-users] Potential Energy Landscape

I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM. The problem I'm facing with the data is the difference between the loading rates of the two approaches. For the MDS the loading rate is around 10 N/s, whereas the AFM

Re: [gmx-users] maybe you are out of quota?

On 21/11/2011 9:02 PM, Vasileios Tatsis wrote: Dear Gromacs Users, The following error messages appear while running MD simulations with Gromacs 4.5.4: - Cannot flush logfile - maybe you are out of quota? - XTC error - maybe you are out of quota? - Cannot read/write checkpoint; corrupt file,

Re: [gmx-users] Topology error

On 21/11/2011 9:18 PM, archana sonawani wrote: Dear Sir/Madam, For orienting the protein and membrane, I have used the .mdp and following topology file: ; ; File 'topol_popc.top' was generated ; By user: jalemkul (502) ; On host:bevany.biochem.vt.edu

Re: [gmx-users] Potential Energy Landscape

On 21/11/2011 10:36 PM, Natalie Stephenson wrote: I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM. The problem I'm facing with the data is the difference between the loading rates of the two approaches. For the MDS the

Re: [gmx-users] Ligand charge assignment

On 21/11/2011 9:28 PM, archana sonawani wrote: Dear Sir/madam, I have a ligand molecule for which I generated the topology file using Prodrg software. As the charges and groupings provided by Prodrg are not much reliable. I need to assign correct charges and groupings for my ligand. I had

[gmx-users] g_helixorient

Hi, I have a peptide inserted in membrane would like to analyze the peptide tilt. The command i have used to do this is : g_helixorient -s .tpr -f .xtc -n .ndx -otilt Index file contains all carbon alpha atoms of the helix. When i plot the tilt.xvg in xmgrace, i simply cannot obtain

Re: [gmx-users] g_helixorient

Hi, have you tried to see the graphic with xmgrace using the flag -nxy? I had the same problem my first time. Best regards. De: Poojari, Chetan c.pooj...@fz-juelich.de Para: gmx-users@gromacs.org gmx-users@gromacs.org Enviado: lunes 21 de noviembre de 2011

Re: [gmx-users] g_helixorient

Hey, try xmgrace -nxy filename.xvg Best wishes Sebastian Am 21.11.2011 15:42, schrieb Poojari, Chetan: Hi, I have a peptide inserted in membrane would like to analyze the peptide tilt. The command i have used to do this is : g_helixorient -s .tpr -f .xtc -n .ndx -otilt Index file

[gmx-users] atomtype OW is not found

 I am running membrane simulation in gromacs using the posted tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html at the step of grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I am usually getting the error that:

[gmx-users] PRODRG charges

Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? In this case, do we treat all ligand atoms as one charge group? Thanks. George -- gmx-users mailing

Re: [gmx-users] atomtype OW is not found

Doaa Ragab wrote: I am running membrane simulation in gromacs using the posted tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html at the step of grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I am usually

Re: [gmx-users] PRODRG charges

g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly

Re: [gmx-users] Poor exchange probability for REMD

The exchange probability will just effect the computational efficiency. It's entirely possible that it won't even effect that, since the dynamics of the replica flow up and down the temperature range may be limited by the dynamics of your protein rather than the exchange frequency and

[gmx-users] removing dihedral

Dear gromacs users, I am trying to build the topology for a protein-ligands system. When I run grompp I obtain 96 of the following errors: ERROR 1 [file topol_Protein_chain_S.itp, line 38658]: No default Proper Dih. types The errors correctly says that dihedral parameters are missing for my

[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

Dear GROMACS users, Is anyone aware of any benchmark analysis about the implementation of the amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in GROMACS and AMBER. I am interested to know in what extend the energies correlate and if the results agree with experimental data.

Re: [gmx-users] removing dihedral

francesco oteri wrote: Dear gromacs users, I am trying to build the topology for a protein-ligands system. When I run grompp I obtain 96 of the following errors: ERROR 1 [file topol_Protein_chain_S.itp, line 38658]: No default Proper Dih. types The errors correctly says that dihedral

[gmx-users] force vs displacement

hello Justin, For afm simulation,I have obtained force vs time and displacemnet vs time plot.how to get force vs displacement plot? please tell. Thanx - This email has been sent using ArithMail at Indian Institute of Information Technology, Allahabad,

Re: [gmx-users] force vs displacement

ibi2010...@iiita.ac.in wrote: hello Justin, For afm simulation,I have obtained force vs time and displacemnet vs time plot.how to get force vs displacement plot? please tell. You have all the data you need in the output files already. You can write a simple script to parse out the

Re: [gmx-users] removing dihedral

I am using parameters already developed for CHARMM. So I guess the parameters are right and I am sure there is no error in the trasformation from CHARMM to GROMACS format. May the option -zero in grompp solve my problem? Il 21/11/2011 21:00, Justin A. Lemkul ha scritto: francesco oteri

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

Is anyone aware of any benchmark analysis about the implementation of the amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in GROMACS and AMBER. I am interested to know in what extend the energies correlate and if the results agree with experimental data. Whether the

Re: [gmx-users] removing dihedral

Francesco Oteri wrote: I am using parameters already developed for CHARMM. So I guess the parameters are right and I am sure there is no error in the trasformation from CHARMM to GROMACS format. May the option -zero in grompp solve my problem? Well, using grompp -zero will bypass the

Re: [gmx-users] removing dihedral

ffbonded.itp is right, grompp misses only a particular dihedral. Everithing is fine for bond, angle and some dihedrals. What exactly means zeroing out all terms for the unknown dihedrals? It means that are not present in tpr or that parameters (i.e reference angle, multiplicity,...) are zero?

[gmx-users] disable-nice

Hi, On page 223 of the 4.5.5 manual the --disable-nice option is mentioned. But configure does not recognize it or --enable-nice=no: configure: WARNING: unrecognized options: --disable-nice configure: WARNING: unrecognized options: --enable-nice scott -- gmx-users mailing list

RE: [gmx-users] density

I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is outlined there and I suspect there are a number of discussions on it within the emailing list archive that you should search. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

[gmx-users] UNK not found

The following is a part of a .pdb file I generated. HETATM 250 C1 UNK 1 18.454 11.417 22.519 1.00 0.00 C HETATM 251 C2 UNK 1 19.297 10.247 22.595 1.00 0.00 C HETATM 252 C3 UNK 1 19.949 9.511 21.410 1.00 0.00 C HETATM

Re: [gmx-users] UNK not found

Janowicz, Adrianna C. wrote: The following is a part of a .pdb file I generated. HETATM 250 C1 UNK 1 18.454 11.417 22.519 1.00 0.00 C HETATM 251 C2 UNK 1 19.297 10.247 22.595 1.00 0.00 C HETATM 252 C3 UNK 1 19.949 9.511

RE: [gmx-users] UNK not found

http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3

Re: [gmx-users] disable-nice

Scott Brozell wrote: Hi, On page 223 of the 4.5.5 manual the --disable-nice option is mentioned. But configure does not recognize it or --enable-nice=no: configure: WARNING: unrecognized options: --disable-nice configure: WARNING: unrecognized options: --enable-nice Probably an old

Re: [gmx-users] removing dihedral

Francesco Oteri wrote: ffbonded.itp is right, grompp misses only a particular dihedral. Everithing is fine for bond, angle and some dihedrals. What exactly means zeroing out all terms for the unknown dihedrals? It means that are not present in tpr or that parameters (i.e reference angle,

[gmx-users] Create gro and top file for hexanoic acid

Dear Sir/Madam, I have tried to creat the gro and top file for acid hexanoic by using the PRODRG server. However, the atom H in -COOH group could not be found and two O atoms are the same. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge

Re: [gmx-users] Create gro and top file for hexanoic acid

cuong nguyen wrote: Dear Sir/Madam, I have tried to creat the gro and top file for acid hexanoic by using the PRODRG server. However, the atom H in -COOH group could not be found and two O atoms are the same. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr

Re: [gmx-users] GROMACS/ORCA QMMM

Does anyone know what is going on with the coordinates of the QM region? Why are they not converted to the correct units? Could anyone point me to the error? Thanks Jose Tusell On Sun, Nov 20, 2011 at 10:06 PM, Jose Tusell jrta1...@gmail.com wrote: Yes.  But where does the code go wrong?  

[gmx-users] Error when try obtain protein energies instead of system energies

Hi, I tried to obtain the energies of protein instead of system energies. However, when I execute the last command, I received the message below: Reading file /home/faccioli/Execute/EESC_AE/1A11/prot_alone.tpr, VERSION 4.5.4 (single precision) Starting 2 threads Making 1D domain decomposition 2

RE: [gmx-users] Error when try obtain protein energies instead of system energies

The error message is stating that your .trr file only has 390 atoms in it, where as the .tpr file has 20524. Those need to match. Where you have made the error, tried to see it, but with all the full paths in your command lines makes it difficult to see what the actually commands are. Look

[gmx-users] glutamic acid protonation

Hi group. I am having a sudden brainfart here and apologize for the silliness of the question. If the first amino acid of your protein is a Glutamic acid, what would you set the protonation status using the -ter option of pdb2gmx? The protein is in 0.1 molar NaCl solution. I know it is basic

Re: [gmx-users] Error when try obtain protein energies instead of system energies

I believe I understood my mistake. In my compute_energy.mdp file, the value of nstep was zero. However, it is necessary to set to 1. I'll make others testes to evaluate my changes. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering

RE: [gmx-users] glutamic acid protonation

pKa = 4.1 Protonation state of the acid group depends on the pH that you are performing the simulation at. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010

Re: [gmx-users] Error when try obtain protein energies instead of system energies

On 22/11/2011 3:34 PM, Rodrigo Faccioli wrote: I believe I understood my mistake. In my compute_energy.mdp file, the value of nstep was zero. However, it is necessary to set to 1. Yes, but that does not affect the system-size mismatch between run input file and trajectory file. Mark

[gmx-users] do_dssp normalization error

Dear Gromacs users, I used do_dssp to calculate the secondary structure of peptide. From the output scount.xvg file, the last column shows the number of residues that is chain separator. At the end of the scount.xvg file, the last line provide the percentage of different secondary

[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

On 11/22/2011 04:02 AM, gmx-users-requ...@gromacs.org wrote: gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Does anyone know what is going on with the coordinates of the QM region? Why are they not converted