[gmx-users] Residue 'NAG' not found in residue topology database

Dear Gromacs Users, My Protein has three N-acetyl glucosamine (NAG) residues, UDP and Mn. I have to simulate this protein. I am using a gromacs version of 4.5.3. When i did pdb2gmx step, i understood that NAG is not present in the residue topology database. I used GROMOS96 53a6 force field as i am

Re: [gmx-users] Gromacs 3.3.3 on Lion Xgrid

On Mar 6, 2012, at 22:03 , Benjamin Hall wrote: Hi I realise this is a question regarding an old version of gromacs on a new OS, but I was hoping that someone could tell me why grompp might fail in 3.3.3 with the following error llvm-gcc-4.2: error trying to exec

Re: [gmx-users] g_select problem (Invalid command line argument:)

Hi Leila, You didn't enclose your selection string, you enclosed some words in your selection string. g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select Close to Protein 'resname' 'SOL' and within 0.25 of group 'Protein' g_select -f com_ta_full_3.xtc -s com_ta_full.tpr

Re: [gmx-users] g_select problem (Invalid command line argument:)

On 08/03/12, leila karami karami.lei...@gmail.com wrote: Dear Justin Thanks for your reply. As you said You need to enclose your selection string within ' ' so it is interpreted as a single string. , I enclosed my selection string: g_select -f com_ta_full_3.xtc -s

Re: [gmx-users] Residue 'NAG' not found in residue topology database

On 08/03/12, pragna lakshmi pragna...@gmail.com wrote: Dear Gromacs Users, My Protein has three N-acetyl glucosamine (NAG) residues, UDP and Mn. I have to simulate this protein. I am using a gromacs version of 4.5.3. When i did pdb2gmx step, i understood that NAG is not present in the

Re: [gmx-users] Gromacs 3.3.3 on Lion Xgrid

On 08/03/12, Esztermann, Ansgar ansgar.eszterm...@mpi-bpc.mpg.de wrote: On Mar 6, 2012, at 22:03 , Benjamin Hall wrote: Hi I realise this is a question regarding an old version of gromacs on a new OS, but I was hoping that someone could tell me why grompp might fail in

[gmx-users] Fwd: charm to gromacs

Actually I solved the problem, I did a mistake in the bond conversion. Actually I found the right formula: k_gromacs = k_charmm**418.4**2 rising form the conversion from angstrom to nanometer -- Messaggio inoltrato -- Da: francesco oteri francesco.ot...@gmail.com Date: 08

[gmx-users] How to input multiple trr files?

Dear Gromacs experts, I am trying to use the following command: g_covar -s file.pdb -f dynamic.trr -o -v However, since my trr file is too large, I have to separately prepared it into dynamic1.trr dynamic2.trr, dynamic3.trr. Would you mind to instruct how to input several trr files, how to

[gmx-users] How to interpret the cosine content result?

Dear Gromacs experts, I did the following steps to calculate the cosine content for my MD simulation. g_covar -s file.pdb -f dynamic.trr -o -v g_anaeig -s file.pdb -f dynamic.trr -v eigvect.trr -proj g_analyze -f proj.xvy -cc -n 8 After the final step, I got a file call coscont.xvg, I

Re: [gmx-users] How to input multiple trr files?

On 08/03/12, a a pat...@hotmail.com wrote: Dear Gromacs experts, I am trying to use the following command: g_covar -s file.pdb -f dynamic.trr -o -v However, since my trr file is too large, I have to separately prepared it into dynamic1.trr dynamic2.trr,

RE: [gmx-users] How to input multiple trr files?

Dear Mark, In fact, I was converting the AMBER trajectories to trr format by VMD. However, my VMD is failed to load so large trajectories files. I guess I can convert several trr files into one trr file. Is it possible to be done with GROMACS? If yes, how can I do it? Many thanks,

[gmx-users] g_energy Kinetic Energy

Dear Gromacs users, After running two different simulations, one Hypercin molecule solvated in water and the other one with 2 Hypericin molecules solved in water as well. After that   I used g_energy to extract the kinetic energy of the first simulation,but the values are  pretty high (it's

RE: [gmx-users] How to input multiple trr files?

On 08/03/12, a a pat...@hotmail.com wrote: Dear Mark, In fact, I was converting the AMBER trajectories to trr format by VMD. Please say this the first time :-) Withholding information makes it hard for you to benefit from what others might know. See

Re: [gmx-users] How to input multiple trr files?

Gromacs is able to load you AMBER trajectory so you don't need to perform any conversion -- Messaggio inoltrato -- Da: a a pat...@hotmail.com Date: 08 marzo 2012 11:46 Oggetto: RE: [gmx-users] How to input multiple trr files? A: gmx-users@gromacs.org Dear Mark, In fact, I was

[gmx-users] a request regarding pdb2gmx and specbond.dat

Hi, The mechanism for specifying special bonds for the pdb2gmx program, using the specbond.dat file (manual section 5.6.7), seems to me not general enough. The characteristic length of the bond is specifiable, but the range of lengths for which a bond is assumed is hardcoded as +-10% of the

Re: [gmx-users] g_energy Kinetic Energy

Hovakim Grabski wrote: Dear Gromacs users, After running two different simulations, one Hypercin molecule solvated in water and the other one with 2 Hypericin molecules solved in water as well. After that I used g_energy to extract the kinetic energy of the first simulation,but the values

[gmx-users] g_select vs trjorder

Dear Tsjerk and Mark Thanks for your time and attention. using g_select -f *.xtc -s *.tpr -n index.ndx -oi -select 'Close to Protein resname SOL and within 0.25 of group Protein' solved my problem. I want to use trjorder -f *.xtc -s *.tpr -n index.ndx -o ordered.pdb -nshell -r 0.25 -na 3 -da 1

[gmx-users] g_select vs trjorder

Dear all Which one of g_select and trjorder is the best for obtaining those water molecules being within x nm of protein? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Umbrella Sampling - Protein Ligand

Dear Gmx Users, Dear Justin, I pulled my ligand away from my protein. Ligand was attached to lower part of my protein, I pulled in Z coordinate it using: ; Run parameters integrator = md ; leap-frog integrator nsteps = 500 ; 2 * 500 = 10 ns dt = 0.002 ; 2 fs tinit = 0 nstcomm = 10 ;

Re: [gmx-users] g_select vs trjorder

leila karami wrote: Dear all Which one of g_select and trjorder is the best for obtaining those water molecules being within x nm of protein? You will have to define what obtaining means. The tools you've mentioned do different things. With g_select, you obtain index groups that tell

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: Dear Gmx Users, Dear Justin, I pulled my ligand away from my protein. Ligand was attached to lower part of my protein, I pulled in Z coordinate it using: ; Run parameters integrator = md ; leap-frog integrator nsteps = 500 ; 2 * 500 = 10 ns dt = 0.002 ; 2

Re: [gmx-users] a request regarding pdb2gmx and specbond.dat

Hi, I agree it could be very useful. You can insert the bond hand-coding it in the topology, but you need also to generate angle and dihedral. This is very boring and error prone. Francesco Il giorno 08 marzo 2012 12:32, Ehud Schreiber schr...@compugen.co.il ha scritto: Hi, ** ** The

[gmx-users] g_select vs trjorder

Dear Justin Thanks for your reply. I know, with g_select, I obtain index groups that tell me which atoms satisfy the given criteria and with trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. But g_select gives an output file

Re: [gmx-users] Umbrella Sampling - Ligand Protein

On Thu, Mar 8, 2012 at 2:18 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, Dear Justin, I pulled my ligand away from my protein. Ligand was attached to lower part of my protein, I pulled in Z coordinate it using: ; Run parameters integrator = md ;

Re: [gmx-users] g_select vs trjorder

leila karami wrote: Dear Justin Thanks for your reply. I know, with g_select, I obtain index groups that tell me which atoms satisfy the given criteria and with trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. But

[gmx-users] g_select vs trjorder

Dear Justin You are wright. The two output files should not be equivalent. If I want to know residue number of water molecules being within x nm of protein, which tool is the best for me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] g_select vs trjorder

Dear Justin If I want to know residue number of water molecules being within x nm of protein, for each frame, which tool is the best for me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Periodic molecules and minimum bonded cut-off

Justin and Mark, Thank you so very much for your time and help. Thank you kindly. Andrew -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

[gmx-users] Read mdcrd from AMBER --- Error Message

Dear Sir/Madam, I learnt that we can use mdcrd from AMBER directly. I have used the following commands. /share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v An error message was obtained. Program g_covar, VERSION 4.0.7Source code file: gmxfio.c, line: 737 Can not open file:md0.mdcrd.xtc Did

Re: [gmx-users] g_select vs trjorder

leila karami wrote: Dear Justin You are wright. The two output files should not be equivalent. If I want to know residue number of water molecules being within x nm of protein, which tool is the best for me? If you simply want to identify which residues they are, then maybe g_dist

Re: [gmx-users] Read mdcrd from AMBER --- Error Message

Hi Catherine, you should install any gromacs *4.5.x*, and then you can use gromacs with each trajectory supported by VMD because gromacs is able to use VMD plugin to perform trajectory reading. Basically: 1) Install the latest gromacs version 2) Install VMD 3) Set the variable VMD_PLUGIN_PATH to

[gmx-users] Radial distribution function by COM

Hello everyone, Is there any way to do a g(r) plot between the COM of a single solute particle, and the COMs of each solvent molecule around it? It seems to only let your choice be the COM for the first pick. Is there any way to do it for both choices? Thanks. -- Best regards, Fabian F.

Re: [gmx-users] Radial distribution function by COM

Fabian Casteblanco wrote: Hello everyone, Is there any way to do a g(r) plot between the COM of a single solute particle, and the COMs of each solvent molecule around it? It seems to only let your choice be the COM for the first pick. Is there any way to do it for both choices? I

[gmx-users] (no subject)

Hi, I want to add 8 of a molecule including 6 atoms. But when I run each of the following commands I System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1948, nrj = 22927 Try 63309box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE

[gmx-users] 'not allocate memory'

Hi, I want to add 8 of a molecule including 6 atoms. But when I run each of the following commands: genbox -ci H.gro -nmol 8 -box 15 15 15 -p topol.top -o H-box.gro genbox -ci H.gro -nmol 8 -box 100 100 100 -p topol.top -o H-box.gro genbox -ci H.gro -nmol 8 -box 150 150 150 -p

Re: [gmx-users] (no subject)

saly jackson wrote: Hi, I want to add 8 of a molecule including 6 atoms. But when I run each of the following commands I System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1948, nrj = 22927 Try 63309box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are

[gmx-users] Martini

Dear Gromacs Specialists, May I ask you to help me for definition of pyrrole, tiofen and aniline in MARTINI coarse-grained force field, Please? I defined them as following: aniline (one benzene ring+NH2) = SC4, SC4, SNd pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1

Re: [gmx-users] Martini

SC5 does not work? Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 8, 2012 at 2:34 PM, dina dusti dinadu...@yahoo.com wrote: Dear

[gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent

Hi, Thank you for your answer. May I ask where I can find the right parameter in gbsa.itp for ions? These should be very basic things in simulation, but I cannot find their parameters anywhere. How do you guys use implicit solvent if you want to have ions inside? Thank you! Bo bo.shuang wrote:

[gmx-users] Martini

Dear Dariush, Thank you very much from your response. Then you tell me that the definition of aniline and pyrrole, is correct? Is your mean about SC5 for tiofen means that it is defined as SC4 and SC5 for tiofen? indeed I had doubt about this definition because S is without H in tiofen. May

Re: [gmx-users] Martini

I think I made a mistake: Aniline: SC4 -SC4 - SNd Pyrrole: SC4 -SNd Tiofen: SC4 - SC5 I am not sure... On Thu, Mar 8, 2012 at 3:24 PM, dina dusti dinadu...@yahoo.com wrote: Dear Dariush, Thank you very much from your response. Then you tell me that the definition of aniline and pyrrole,

[gmx-users] g_helix not recognizing protein backbone

I am running g_helix on a run involving a 37 residue protein in the charmm force field. It has two long alpha helical segments. I have tried running g_helix with many different variations of commands and getting rid of PBC effects, but I always get the same error: Checking group System There are

Re: [gmx-users] Read mdcrd from AMBER --- Error Message

On 9/03/2012 3:40 AM, a a wrote: Dear Sir/Madam, I learnt that we can use mdcrd from AMBER directly. I have used the following commands. /share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v An error message was obtained. Program g_covar, VERSION 4.0.7 Source code file: gmxfio.c, line:

Re: [gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent

On 9/03/2012 7:19 AM, bo.shuang wrote: Hi, Thank you for your answer. May I ask where I can find the right parameter in gbsa.itp for ions? These should be very basic things in simulation, but I cannot find their parameters anywhere. How do you guys use implicit solvent if you want to have

Re: [gmx-users] g_helix not recognizing protein backbone

On 9/03/2012 8:50 AM, MPID wrote: I am running g_helix on a run involving a 37 residue protein in the charmm force field. It has two long alpha helical segments. I have tried running g_helix with many different variations of commands and getting rid of PBC effects, but I always get the same

Re: [gmx-users] g_helix not recognizing protein backbone

MPID wrote: I am running g_helix on a run involving a 37 residue protein in the charmm force field. It has two long alpha helical segments. I have tried running g_helix with many different variations of commands and getting rid of PBC effects, but I always get the same error: Checking group

[gmx-users] 'not allocate memory'

Hi I think the error is not a reason of less memory of my computer. Because in a supercomputer I see the hollowing error too. Genbox could be run if I choose the number of atoms less than 5000. Thanks Saly Try 824box_margin = 0.45 overlap: Neighborsearching with a cut-off of 0.45 Table

Re: [gmx-users] 'not allocate memory'

saly jackson wrote: Hi I think the error is not a reason of less memory of my computer. Because in a supercomputer I see the hollowing error too. genbox is not parallelized, and thus cannot make use of multiple processors and the memory on them. Genbox could be run if I choose the

[gmx-users] Re: g_helix not recognizing protein backbone

It worked! Thanks a lot, it was just changing HN to H in the itp file and re-running grompp to make a new tpr file. Thanks a lot. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-helix-not-recognizing-protein-backbone-tp4560173p4560255.html Sent from the GROMACS Users Forum

Re: [gmx-users] I need a tutorial for gromacs-4.0.5

On 9/03/2012 12:52 PM, Dialing Pretty wrote: Dear Mark, I have tried to install the most recent version of gromacs by cygwin, but I fail. But I have successfully installed the 4.0.5 version. However I find the on-line tutorial is only suitable for the new version. Will you please tell me

Re: [gmx-users] Recommended protocol for cooling down temperature in 50 K steps

Andrew DeYoung wrote: Hi, I have a system that I would like to equilibrate in the NPT ensemble at high temperature, and then, in subsequent equilibration steps, cool down in steps of 50 K. Thus, in the first step, I will use gen_vel = yes, while in all subsequent steps, I will use gen_vel =

Re: [gmx-users] Recommended protocol for cooling down temperature in 50 K steps

On 9/03/2012 1:08 PM, Justin A. Lemkul wrote: Andrew DeYoung wrote: Hi, I have a system that I would like to equilibrate in the NPT ensemble at high temperature, and then, in subsequent equilibration steps, cool down in steps of 50 K. Thus, in the first step, I will use gen_vel = yes,

[gmx-users] Cluster analysis

Hello, I would like to do cluster analysis in gromacs on my system which consists of a polymer and solvent . I would like to know how the solvent molecule surrounds around polymer and how many. Can anybody help me out that how to start with or use g_cluster or g_clustsize in gromacs. Also there

[gmx-users] Using CHARMM27 with TIP4PEW

Hi, I'm interested in using CHARMM27 with the TIP4PEW water model. However, only TIP4P is available by default. Are their any fundamental barriers to my editing/adding to the files in the charmm27.ff folder to enable TIP4PEW? Is there any fundamental reason why TIP4PEW isn't enabled, other than

[gmx-users] LINCS Fatal error

Hi GROMACS specialist, I am using MARTINI forcefield, My mdp file contain following parameter constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 90 gromacs output is Step 0, time 0 (ps) LINCS WARNING relative constraint

[gmx-users] Atom O5 not found in residue seq.nr. 1 while adding atom

Dear Gromacs Users, I need to simulate a protein that has N-acetyl glucosamine (NAG). Since NAG residue is not present in residue topology file, first of all i added NAG parameters to aminoacids.rtp file. I am following this link *

[gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

I forgot to mention that i am using OPLS-AA/L all-atom force field. On Fri, Mar 9, 2012 at 11:21 AM, pragna lakshmi pragna...@gmail.com wrote: Dear Gromacs Users, I need to simulate a protein that has N-acetyl glucosamine (NAG). Since NAG residue is not present in residue

Re: [gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

On 9/03/2012 4:56 PM, pragna lakshmi wrote: I forgot to mention that i am using OPLS-AA/L all-atom force field. On Fri, Mar 9, 2012 at 11:21 AM, pragna lakshmi pragna...@gmail.com mailto:pragna...@gmail.com wrote: Dear Gromacs Users, I need to simulate a protein that

Re: [gmx-users] LINCS Fatal error

On 9/03/2012 4:27 PM, rama david wrote: Hi GROMACS specialist, I am using MARTINI forcefield, My mdp file contain following parameter constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 90 gromacs output is Step 0, time 0 (ps)

Re: [gmx-users] Martini

Thank you very much from your response. Best Regards Dina From: Dariush Mohammadyani d.mohammady...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, March 9, 2012 1:05 AM Subject: Re:

[gmx-users] Segmentation fault

Hi , Thank you for help. I solve my problem for LINCS error But now I have another problem after mdrun command gromacs output Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Martini system from nap.pdb' 5000 steps,100.0 ps. step 0Segmentation fault Please give the valuable

Re: [gmx-users] Segmentation fault

On 9/03/2012 6:24 PM, rama david wrote: Hi , Thank you for help. I solve my problem for LINCS error But now I have another problem after mdrun command gromacs output Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Martini system from nap.pdb' 5000 steps,100.0 ps. step

Re: [gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

Thank u so much Mark. Is there any parameterization to mention forcefield and co ordinates in aminoacids.rtp in the fields of atoms, bonds (like C1opls_195 +0.3651 ). I checked the co ordinates in .pdb and .rtp files. Both are not the same. On Fri, Mar 9, 2012 at 11:56 AM, Mark

[gmx-users] g_fg2cg

Dear Andrzej, I checked all of files and there is no problem in them. I before did it (g_fg2cg) for one surfactant and was performed correctly. I want to calculate the center of mass of atoms in one bead manually (each CG bead is at the center of mass of the FG atoms that map to it) for cg.gro,