Re: [gmx-users] Top file

On 6/26/12 1:52 AM, Shima Arasteh wrote: Dear gmx users, I have a problem about the topology output of pdb2gmx. There is a formyl residue as N-terminal in my .pdb file. I know that the pdb file is correct in agreement with RCSB .pdb files. The force field I have to use is gmx ( I need

[gmx-users] Rotation aroud the z axis

Hi everybody, I use the tutorial proposed by gromacs for a membrane simulation. But when I do this and look at my protein in the membrane after the Pack the lipids around the protein step its orientation in the membrane is wrong. So my question is: how can I rotate the protein around the z axis?

Re: [gmx-users] Rotation aroud the z axis

On 6/26/12 8:36 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I use the tutorial proposed by gromacs for a membrane simulation. But when I do this and look at my protein in the membrane after the Pack the lipids around the protein step its orientation in the membrane is

[gmx-users] ewald_geometry 3dc with wall gives high pressure

Zifeng Li lizife...@gmail.com Dear Gromacs users, I want to compress a polymer slab and solvate it with water to exam the interface between them. To prevent the polymer from crossing the interface along z direction, I compress it using 2 walls by moving them towards each other a little

[gmx-users] PBC

Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x axis distance is more than L/2) and it will come inside the box from other side (distance-L). Distance before the pbc should be same or it will be different from center. Thanks Nilesh --

[gmx-users] H-atoms in .hdb file

 Dear gmx users, However this H-atom is defined in .hdb file of force field before, why sometimes I need to add a H-atom to the pdb on my own? Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] H-atoms in .hdb file

On 6/26/12 10:25 AM, Shima Arasteh wrote: Dear gmx users, However this H-atom is defined in .hdb file of force field before, why sometimes I need to add a H-atom to the pdb on my own? A properly constructed .hdb entry eliminates the need for manual introduction of H atoms. If you

Re: [gmx-users] H-atoms in .hdb file

Thanks for you reply. As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb . In .rtp file:  [ atoms ] C   CH1  0.380  0 O O -0.380  0  [ bonds ] C  O    C +N      [angles ]   ai   

Re: [gmx-users] H-atoms in .hdb file

On 6/26/12 10:44 AM, Shima Arasteh wrote: Thanks for you reply. As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb . In .rtp file: [ atoms ] C CH1 0.380 0 O O -0.380 0 [ bonds ]

Re: [gmx-users] PBC

Hey Nilesh, Distance to where? Just think of your PBC in one dimension as being on a circle. Cheers, Tsjerk On Tue, Jun 26, 2012 at 4:26 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x

Re: [gmx-users] H-atoms in .hdb file

Oh, you're right. Those are the contents of the tdb file. I wrote hdb by mistake! sorry! :-) Thanks so much Justin. NOW, 1. I made an aminoacids.dat file and added FOR to other residues, as below: 49 ABU ACE    AIB ALA  ARG  ARGN ASN ASN1  ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA FOR GLN 

Re: [gmx-users] H-atoms in .hdb file

I tried again as below: 1. defined FOR in .rtp file 2. defined FOR in aminoacids.dat file. 3. chose NH2 as N-Terminal and then got this topology for FOR and VAL: ; residue   0 FOR rtp FOR  q  0.0 1    CH1  0    FOR  C  1   0.38 13.019   ; qtot 0.38 2  O  

Re: [gmx-users] H-atoms in .hdb file

On 6/26/12 11:36 AM, Shima Arasteh wrote: I tried again as below: 1. defined FOR in .rtp file 2. defined FOR in aminoacids.dat file. 3. chose NH2 as N-Terminal and then got this topology for FOR and VAL: ; residue 0 FOR rtp FOR q 0.0 1CH1 0FOR C 1

Re: [gmx-users] H-atoms in .hdb file

OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it?   Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012

Re: [gmx-users] H-atoms in .hdb file

On 6/26/12 11:47 AM, Shima Arasteh wrote: OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it? Dangling bond errors were introduced as part of the output in Gromacs 4.5. The aminoacids.dat file was only used by older (4.0.x and

[gmx-users] Lipid-protein simulation....

Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box

[gmx-users] Re: Lipid-protein simulation....

On Tue, Jun 26, 2012 at 9:32 PM, rama david ramadavidgr...@gmail.com wrote: Hi Gromacs Friends,  I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system  to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website.  I

[gmx-users] number of gauche - trans transitions with CHARMM36 and AMBER force fields

Dear all, I would like to compute the number of gauche -- trans transitions (per ns) for for several alkanes. I know that I can use g_angle with -ot flag. But in the manual it is stated that this command works only for dihedrals with multiplicity 3. In CHARMM36 force field, for

Re: [gmx-users] Lipid-protein simulation....

On 6/26/12 12:02 PM, rama david wrote: Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial

[gmx-users] What's the effect of non-neotron charge group?

Dear Gromacs users, I use gromacs version 4.5.4 and build residue of my own polymers which has a ester group (COOR). From aminoacids.atp database, I found the partial charge of each atom, where the carbolic group COO- is not neutron and has to be neutralized by a methyl group. Should I consider

[gmx-users] What does --enable-fahcore mean?

Hi, all, I am wondering what the --enable-fahcore option of configure means. I got the explanation from configure --help of create a library with mdrun functionality, while it is not very clear to me. Best Regards, Kai -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] What does --enable-fahcore mean?

It only matters for running on Folding@Home. For other users of gromacs, it doesn't do anything. On Tue, Jun 26, 2012 at 3:50 PM, Bao Kai paeanb...@gmail.com wrote: Hi, all, I am wondering what the --enable-fahcore option of configure means.  I got the explanation from configure --help of

[gmx-users] wrong distances with g_dist

Hi, I try to calculate distance between two atoms with g_dist. Somewhat I get distance lower than actual. Here there are coordinates of the two atoms (PDB format) ATOM702 CZ ARG X 45 5.930 9.230 41.740 0.00 0.00 ATOM 2751 CA PHE X 177 41.710 45.000 27.180 0.00

[gmx-users] Unusual g_order with CHARMM36

Dear Gmx users, anyone which used the CHARMM36 (available for downloading in the Gromacs website) for simulating a POPC, POPE or whatever POxx membrane in Gromacs has found an unusual behavior in the Oleyl chain when it comes to the deuterium order parameter (Scd)? Let me explain a little

[gmx-users] Atoms get frozen with Nose Hoover thermostat with Parrinello-Rahman barostat for a system of an ion of charge +2 in flexible water molecules

Dear Gromacs users, I am having a very strange problem with Nose Hoover thermostat with Parrinello-Rahman barostat NPT simulations for a system of an ion of charge +2 in flexible water molecules. Flexible water is taken from J. Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877.

[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

Hi Gromacs Friends,     I am doing Justin-lipid tutorialer http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html In these the npt.mdp has a parameter refcoord_scaling = com Why these parameter is introduced in NPT of lipid-protein simulation  and not use in Lysozyme in