Re: [gmx-users] line longer than 4095 - a bug?

On 11/05/2012 6:43 PM, Marzinek, Jan wrote: Dear Gmx Users, Many of you probably faced an error: "An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' " As I noted this error comes from the changes in the topo

Re: [gmx-users] dipole moment

Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. On May 13, 2012, at 15:11, dina dusti wrote: > Dear Justin, > > Thank you very much from your response. > > Best Regards

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Thanks for your suggestions. Now, I think that it's better to add the N atom of next residue  to the .pdb file and then add hydrogen atoms to its .mol2 format. Because when I open formyl.pdb in  chimera software and add hydrogens to it, it becomes an formaldehyde and then I get the a wrong param

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 14/05/2012 6:00 PM, Shima Arasteh wrote: Thanks for your suggestions. Now, I think that it's better to add the N atom of next residue to the .pdb file and then add hydrogen atoms to its .mol2 format. Because when I open formyl.pdb in chimera software and add hydrogens to it, it becomes an

[gmx-users] unsubcribes

-- 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-u

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Thanks for your suggestions. This is the .itp file got from the SwissParam. [ atoms ] ; nr type resnr resid atom cgnr charge mass   1 C=O  1  LIG C   1  0.5700  12.0110    2 O=C  1  LIG O   2 -0.5700  15.9994    3 NC=O 1  LIG N   3 -0.7301  14.0067    4 CR   1  LIG CA  4  0.194

[gmx-users] index files for trjconv -sub

Dear Gromacs users, I'm new to molecular dynamics and I face some problems with the analysis of my trajectories. I intend to use the trjconv utility to extract frames from my trajectories. Each trajectory can contain several frames that belong to different clusters. To do this I create an .ndx f

Fw: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

  Thanks for your suggestions. Now I got the .itp file for frmyl+valine(the next residue). This is the .itp file got from the SwissParam. [ atoms ] ; nr type resnr resid atom cgnr charge mass   1 C=O  1  LIG C   1  0.5700  12.0110    2 O=C  1  LIG O   2 -0.5700  15.9994    3 NC=O 1  LI

[gmx-users] Regarding errors

Dear all gromacs users, I tried the grompp and i got the following error."number of coordinates in coordinate file (4INS_b4ion.gro, 90396) does not match topology (4INS.top, 90393)". Is there any explanation why is this happ

[gmx-users] doubts on gen-pairs

Dear gmx-users, I have some doubts on the manual pages. Kindly help to understand the same. Section 5.7.1 Page 129 1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ. Is there any way that I can see/write

RE: [gmx-users] Regarding errors

Dear Suryanarayana Seera Please check the itp files mentioned in the topol.top and what u used in your commands. Especially check the solvent model. May be you have not changed that in the topol.top file. From: gmx-users-boun...@gromacs.org [gmx-users-boun...

Re: [gmx-users] dipole moment

On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: > > > Hi, > > > You do not need to use the polarizable martini water model to > calculate the dipole of molecules. Or I am missing a point here! > > > g_dipole should do the work > > XAvier. > Hi, I want to point to another probl

Re: [gmx-users] doubts on gen-pairs

On Mon, 2012-05-14 at 11:55 +0200, Bala subramanian wrote: > Dear gmx-users, I have some doubts on the manual pages. Kindly help to > understand the same. > > > Section 5.7.1 Page 129 > > 1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not > present in the pair list from normal Len

Re: [gmx-users] dipole moment

Interesting ... do you have a reference for this? XAvier. On May 14, 2012, at 12:01 PM, Dommert Florian wrote: On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a

Re: [gmx-users] dipole moment

On Mon, 2012-05-14 at 12:27 +0200, XAvier Periole wrote: > Interesting ... > > do you have a reference for this? > Sure, a detailed discussion about charges for the liquid phase and results for molecular ionic liquids are published in: http://dx.doi.org/10.1039/C1FD00051A and http://pubs.acs

[gmx-users] Virtual Sites - remove from GRO

Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as VMD write the file using atoms not recognized by pd

Re: [gmx-users] Virtual Sites - remove from GRO

On 5/14/12 8:42 AM, Steven Neumann wrote: Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as VMD w

Re: [gmx-users] Virtual Sites - remove from GRO

On 14/05/2012 10:42 PM, Steven Neumann wrote: Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as

Re: [gmx-users] Virtual Sites - remove from GRO

On Mon, May 14, 2012 at 1:51 PM, Mark Abraham wrote: > On 14/05/2012 10:42 PM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> i run the implicit simulation with virtual sites on the hydrogen of my >> protein. Now I want to extract coordinates and run another simulation (in >> explicit solvent).

[gmx-users] validation of a .rtp file

 Dear gmx users, I made an .rtp file for formyl. First of all, how can I be sure that what I built, is correct? Sincerely, Shima-- 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/

[gmx-users] fatal error: missing H atom in .pdb file

Dear gmx users, I changed the aminoacids.rtp file recently. Now, when I run pdb2gmx, I get the fatal error: atom H is missing in residue For 0 in the pdb file You might need to add atom H to the hydrogen database of building block For in the file aminoacids.hdb -Is it may as a

[gmx-users] Test Particle Insertion

Dear Gmx Users, Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg files consists of: @ s0 legend "-kT log(/)" @ s1 legend "f. -kT log" @ s2 legend "f. " @ s3 legend "f. V" @ s4 legend "f. " @ s5 legend "f. " @ s6 legend "f. " @ s7 legend "f. " @ s8 legend "f. " @

Re: [gmx-users] Test Particle Insertion

On 5/14/12 11:53 AM, Steven Neumann wrote: Dear Gmx Users, Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg files consists of: @ s0 legend "-kT log(/)" @ s1 legend "f. -kT log" @ s2 legend "f. " @ s3 legend "f. V" @ s4 legend "f. " @ s5 legend "f. " @ s6 legend

Re: [gmx-users] validation of a .rtp file

On 5/14/12 10:43 AM, Shima Arasteh wrote: Dear gmx users, I made an .rtp file for formyl. First of all, how can I be sure that what I built, is correct? There are two levels of correctness. Level 1 is the syntactic correctness of the .rtp entry itself, which can be verified with an under

Re: [gmx-users] fatal error: missing H atom in .pdb file

On 5/14/12 11:19 AM, Shima Arasteh wrote: Dear gmx users, I changed the aminoacids.rtp file recently. Now, when I run pdb2gmx, I get the fatal error: atom H is missing in residue For 0 in the pdb file You might need to add atom H to the hydrogen database of building block For in the file amin

[gmx-users] fly some lipids to water

Dear Users, I am simulation bilayer composed of 81 DOPC and 21 cardiolipin (CL) in a box size 6*6*20 (nm^3). For making this system I used DOPC system with a zero surface tension and then I replaced each DOPC with one CL. Now, I got strange result, after long run, some of lipid (most of them are

Re: [gmx-users] how to use the triplets index file generated by g_hbond

Hi Justin, Thank you for the perl script. But I wonder now why there is a difference between what shows in the hbmap.xpm file and the summary_HBmap.dat generated. For example, I found many occurrences of the second to last H-bond in the 20hbmap.xpm file attached (visualized by GIMP), but in the s

[gmx-users] Atom Names or Atom Types in the force field paramerization

Hello I saw that in my force field parametrization I wrote the atom names and not the atom types in the blocks like bonds, angles and so on. Could this be a problem? Should I write the atom types in the blocks? Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.

Re: [gmx-users] how to use the triplets index file generated by g_hbond

The first entry in summary_HBmap.dat is index zero (i.e., the "bottom" of the plot area). So the results look fine to me. -Justin On 5/14/12 1:02 PM, Yun Shi wrote: Hi Justin, Thank you for the perl script. But I wonder now why there is a difference between what shows in the hbmap.xpm file

Re: [gmx-users] fly some lipids to water

On 5/14/12 12:24 PM, Dariush Mohammadyani wrote: Dear Users, I am simulation bilayer composed of 81 DOPC and 21 cardiolipin (CL) in a box size 6*6*20 (nm^3). For making this system I used DOPC system with a zero surface tension and then I replaced each DOPC with one CL. Now, I got strange resul

Re: [gmx-users] Atom Names or Atom Types in the force field paramerization

On 5/14/12 2:27 PM, Lara Bunte wrote: Hello I saw that in my force field parametrization I wrote the atom names and not the atom types in the blocks like bonds, angles and so on. In what file? Could this be a problem? Should I write the atom types in the blocks? That depends on the a

Re: [gmx-users] Atom Names or Atom Types in the force field paramerization

Hi Justin In my flamol.rtp file that I create in my force field order CHARMM27 Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 20:32 Montag, 14.Mai 2012 Betreff: Re: [gmx-users] Atom Names or Atom Typ

Re: [gmx-users] Atom Names or Atom Types in the force field paramerization

On 5/14/12 2:34 PM, Lara Bunte wrote: Hi Justin In my flamol.rtp file that I create in my force field order CHARMM27 Atom names are correct in the .rtp file. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, V

[gmx-users] Question about drift in positions of frozen atoms

Hi, I am using freeze groups to hold the x, y, and z positions of specified atoms fixed (to roughly simulate a fixed surface). I would like to keep the positions of atoms of residuetypes "AT1" and "AT2" fixed. So, in my .mdp file, I have the following keywords pertaining to "freeze": freezegrp

[gmx-users] Atom Types in ffbonded.itp

Hello I want to write my parameters in the ffbonded.itp file in the CHARMM27 force field folder. I wrote my atom types in this file. This atom types are defined by me in atomtypes.dat grompp gives me an error  Fatal error: Unknown bond_atomtype for all my atom types. Do I have to declare that

Re: [gmx-users] Atom Types in ffbonded.itp

On 5/14/12 4:38 PM, Lara Bunte wrote: Hello I want to write my parameters in the ffbonded.itp file in the CHARMM27 force field folder. I wrote my atom types in this file. This atom types are defined by me in atomtypes.dat There is no atomtypes.dat that is read by any Gromacs program, and at

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

Hi All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like [ angles ] ;  ai    aj    ak funct    c0    c1  

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

On 5/14/12 5:15 PM, Lara Bunte wrote: Hi All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like [ angles ] ; aiajak f