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
Dear gmx users,
Where can I find residuetypes.dat file? I couldn't find this in gmx forcefied.
Thanks in advance.
Sincerely,
Shima
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http://www.gromacs.org/Suppor
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
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.
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
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
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
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
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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
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
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
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
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
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
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
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
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
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
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
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 ]
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
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
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
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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
--
>> 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
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
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?
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
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