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 to

[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 i

[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 >> oth

[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 ar

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 wrote: > Hello, > > I have question about periodic boundary condition. Suppose if one atom is > going out of the box (x axis distance is mo

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 0.3

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 To: Discussion list for GROMACS users Cc: Sent: Tuesday, June 26, 2012 8:09 PM Subject: Re: [gmx-users] H-atoms

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 e

[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 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 periodici

[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 exampl

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 i

[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 th

[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 http://lists.gromacs.or

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 wrote: > Hi, all, > > I am wondering what the --enable-fahcore option of configure means.  I > got the explanation from configure --help of "create a library

[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 0.0

[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 furth

[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

[gmx-users] residuetype.dat

Dear gmx users, Where can I find residuetypes.dat file? I couldn't find this in gmx forcefied. Thanks in advance.   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/Suppor

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

Thanks for your replies. I found the residuetypes.dat file in top directory of GROMACS package. I need to add the FOR to this file. But it's question for me where am I supposed to set the residuetypes.dat file? In FF folder existed in my working directory?   Sincerely, Shima - Original Mes