Re: [gmx-users] position restraint and pdb

Bhawana Gupta wrote: hello everyone, pls tell me that whether we can use gromacs for simulating pdb with 3 or 4 residue. Yes. You can use GROMACS to simulate traffic if you want to. :-) As i had done it with 4 residue with blocking group. But then i got the error for rvdw and rlist as they

[gmx-users] position restraint and pdb

hello everyone, pls tell me that whether we can use gromacs for simulating pdb with 3 or 4 residue. As i had done it with 4 residue with blocking group. But then i got the error for rvdw and rlist as they should be nearer to cutoff value. So instead of decreasing the value of rvdw. i increased my

Re: [gmx-users] Re: High frequency output slow down the simulation?

xianghong qi wrote: Hello, all: I compare the two simulations with different output frequency for .xtc file in same machine. One with low frequency runs much faster than the one with high frequency. Is that reasonable? I think the frequency shouldn't affect the simulation speed. Anyone

[gmx-users] Re: High frequency output slow down the simulation?

Hello, all: I compare the two simulations with different output frequency for .xtc file in same machine. One with low frequency runs much faster than the one with high frequency. Is that reasonable? I think the frequency shouldn't affect the simulation speed. Anyone has idea about this situation

Re: [gmx-users] g_rms

Tatsiana Kirys wrote: Hi, i got strange results using g_rms. Does it by default uses mass weighting for superposition? I wrote my own script to calculate rmsd without mass weighting and it gives different results then using g_rms. If it uses mass weighting for superposition how not not use it?

[gmx-users] g_rms

Hi, i got strange results using g_rms. Does it by default uses mass weighting for superposition? I wrote my own script to calculate rmsd without mass weighting and it gives different results then using g_rms. If it uses mass weighting for superposition how not not use it? i tried select "-mw

Re: [gmx-users] Simulation of difloromethane

Polavarapu, Abhigna wrote: Hi all, I am just running a test simulation for normal modes. I am unable to create a topology file for diflormethane as gromacs say "unrecognized MOL residue type". I created it manually but now it says " Invalid order for directive moleculetype, file ""t

[gmx-users] Simulation of difloromethane

Hi all, I am just running a test simulation for normal modes. I am unable to create a topology file for diflormethane as gromacs say "unrecognized MOL residue type". I created it manually but now it says " Invalid order for directive moleculetype, file ""topol.top"", line 17". Please t

Re: [gmx-users] Water model => amber port to gromacs

Chih-Ying Lin wrote: HI Here are the links. Water model => amber port to gromacs http://www.gromacs.org/pipermail/gmx-users/2007-June/027817.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027823.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027840.html The two step

[gmx-users] Water model => amber port to gromacs

HI Here are the links. Water model => amber port to gromacs http://www.gromacs.org/pipermail/gmx-users/2007-June/027817.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027823.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027840.html The two steps are shown on the above

Re: [gmx-users] Re: .xtc file is incomplete

Thanks so much, Chris. I will check wiki. -Xianghong Qi On Fri, Nov 7, 2008 at 10:44 AM, <[EMAIL PROTECTED]> wrote: > We have experienced this with NFS delay problems if you try to access the > fie before it is completely written. On our most frustrating server, it can > take up to an hour for th

Re: [gmx-users] freeze group gives Segmentation fault

[EMAIL PROTECTED] wrote: Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. We're not mind-readers :-) Why do you think it's not working? What do you see on stdout? In the various output files? Plea

Re: [gmx-users] mdp file

He, Yang wrote: Hi Mark, This is what I got when I use the command gmxcheck: Checking file traj.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 34 Last frame 1 time0.100 Item#frames Timestep (ps) Step 20.1 Time

[gmx-users] freeze group gives Segmentation fault

Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. Please note my mdp-file's attached Ilona ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ;

[gmx-users] Re: .xtc file is incomplete

We have experienced this with NFS delay problems if you try to access the fie before it is completely written. On our most frustrating server, it can take up to an hour for the .xtc to be written in rare cases. For us, the biggest problem is when the .trr and .edr are completely written but

[gmx-users] Spatial distribution

I wrote g_spatial and it should produce a spatial distribution function. However, it's rather complicated to use. Did you follow the directions in g_spatial -h ? There are about 10 steps to use it. It is so complicated on purpose in order to give the user full flexibility, but this means th

Re: Re: [gmx-users] rmsd on homologous protein structure

tahnk you i'll try that ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list.

RE: [gmx-users] mdp file

Hi Mark, This is what I got when I use the command gmxcheck: Checking file traj.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 34 Last frame 1 time0.100 Item#frames Timestep (ps) Step 20.1 Time 2

[gmx-users] MD run, polarizable molecules, EM did not converge

Hello all. I've been searching the archives with no luck so here goes: I am using shell molecular dynamics to simulate a hydroxide ion dissolved in water. I have been using the steepest descent minimizer (tried in the range from 30 to 70 steps) to minimize the system, but I'm not capa

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms

Re: [gmx-users] Spatial distribution

Gadzikano Munyuki wrote: I want to analyse the solvent around a peptide . I used g_sdf and the output that i am getting (i.e the refmol.gro) does not have the whole peptide molecule but just the residues that i use to define the coordinate system . I then tried to use g_spatialbut its doing s

Re: [gmx-users] Misunderstandings with g_rms

Jochen Hub wrote: DimitryASuplatov wrote: Hello, I am sorry for this stupid question. Lets say I have an index file of all chain A atoms. I want to calculate RMS of chain A _backbone_ only. I run g_rms. It asks two questions: 1/ Select group for least squares fit 2/ Select group for RMSD calc

Re: [gmx-users] Running MDS over docked poses

vivek sharma wrote: Hi Andreas, Thanks for your response. But I am not finding option for AMBER forcefield in gromacs (during pdb2gmx step). which of the 9 force-field I should use for the same. You have to download and install the ffamber ports: http://chemistry.csulb.edu/ffamber/ -Jus

Re: [gmx-users] about porse.itp

Bhawana Gupta wrote: Dear gmx-users, i made earlier asked this question .but there is a problem. first i got the error: --- Program grompp, VERSION 4.0 Source code file: futil.c, line: 527 Fatal error: Library file posre.itp not found in cu

Re: [gmx-users] prodrg

Bhawana Gupta wrote: hello everyone, Pls tell me whether we can use PRODRG server only for generating peptides with unusual amino acid through JME or it can be used for the peptides having usual amino acid. PRODRG is most useful in obtaining topologies for small molecules. You might use

Re: [gmx-users] Misunderstandings with g_rms

DimitryASuplatov wrote: > Hello, > > I am sorry for this stupid question. > > Lets say I have an index file of all chain A atoms. I want to calculate > RMS of chain A _backbone_ only. > > I run g_rms. It asks two questions: > 1/ Select group for least squares fit > 2/ Select group for RMSD calcu

Re: [gmx-users] Running MDS over docked poses

Hi Andreas, Thanks for your response. But I am not finding option for AMBER forcefield in gromacs (during pdb2gmx step). which of the 9 force-field I should use for the same. With Thanks, Vivek 2008/11/7 Kukol, Andreas <[EMAIL PROTECTED]> > Hi, > > Autodock4 uses the AMBER forcefield, so that w

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atom

[gmx-users] Spatial distribution

I want to analyse the solvent around a peptide . I used g_sdf and the output that i am getting (i.e the refmol.gro) does not have the whole peptide molecule but just the residues that i use to define the coordinate system . I then tried to use g_spatialbut its doing something very different and

[gmx-users] Misunderstandings with g_rms

Hello, I am sorry for this stupid question. Lets say I have an index file of all chain A atoms. I want to calculate RMS of chain A _backbone_ only. I run g_rms. It asks two questions: 1/ Select group for least squares fit 2/ Select group for RMSD calculation To the best of my understanding, I s

[gmx-users] about porse.itp

Dear gmx-users, i made earlier asked this question .but there is a problem. first i got the error: --- Program grompp, VERSION 4.0 Source code file: futil.c, line: 527 Fatal error: Library file posre.itp not found in current dir nor in default

Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

Right! Thanks again Berk. Caterina 2008/11/7 Berk Hess <[EMAIL PROTECTED]>: > Hi, > > For the moment you can use editconf of 3.3 > or copy a cryst1 entry (one of the first lines) from another pdb file > into you pdb input file, editconf will then write the correct box in the > output pdb. > > Berk

RE: [gmx-users] editconf/genbox problem in Gromacs 4.0

Hi, For the moment you can use editconf of 3.3 or copy a cryst1 entry (one of the first lines) from another pdb file into you pdb input file, editconf will then write the correct box in the output pdb. Berk > Date: Fri, 7 Nov 2008 12:13:55 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@groma

Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

Many thanks to Bert and Xavier. >> Dear gmx-users, >> >> I have encountered a similar editconf/genbox problem posted by Matt >> Danielson on 14 October: >> I 'm using Gromacs 4.0 (installed on MacOS). >> >> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o >> may_protein_box.pdb > > use

[gmx-users] prodrg

hello everyone, Pls tell me whether we can use PRODRG server only for generating peptides with unusual amino acid through JME or it can be used for the peptides having usual amino acid. whether it is necessary to use pdb2gmx for peptide containing usual amino acid or we can do it with PRODRG serve

Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

On Fri, 7 Nov 2008 11:23:14 +0100 "Caterina Arcangeli" <[EMAIL PROTECTED]> wrote: Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -

RE: [gmx-users] editconf/genbox problem in Gromacs 4.0

Hi, This is a known bug in 4.0. It has been fixed for 4.0.1, which will hopefully be released today. Berk > Date: Fri, 7 Nov 2008 11:23:14 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] editconf/genbox problem in Gromacs 4.0 > > Dear gmx-users, > > I have

[gmx-users] editconf/genbox problem in Gromacs 4.0

Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb The output from editconf does not report errors, but I noted t

Re: [gmx-users] missing of methyl at N-terminal

thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms while sortin

RE: [gmx-users] Running MDS over docked poses

Hi, Autodock4 uses the AMBER forcefield, so that would be a good starting point for gromacs as well. In order to set the temperature for a particular group 1) you generate an index file containing all the atoms in your GROUP 2) in your mdp-file specify GROUP as a separate temperature coupling gr

[gmx-users] Running MDS over docked poses

Hi There, I am trying to run MDS over some docked result generated by Autodock4, but I am not sure of the forcefield I should use. If anybody have tried doing it before, please guide me for the same. For generating topology of ligand, I am using PRODRG server, which has limited option for forcefie

Re: [gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

Chih-Ying Lin wrote: HI BR- ion is defined in FF_OPLS. Could I mix two force fields, FF_Gromos 96 and FF_OPLS, in my system? ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_402 Br- 35 79.90400-1.000

[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

HI BR- ion is defined in FF_OPLS. Could I mix two force fields, FF_Gromos 96 and FF_OPLS, in my system? ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_402 Br- 35 79.90400-1.000 A4.62376e-01 3.7

Re: [gmx-users] Water model => amber port to gromacs

Chih-Ying Lin wrote: Hi Water model => amber port to gromacs The two steps are shown on the archive. 1. #include ffamber_tip*pin the .top file 2. include an #ifdef_FF_AMBER statement in tip*p.itp If you want others' opinions for free, please provide links - and test them first to see that

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by