Hi there,
Acpype does the conversion for you and the results from their own testing
are here:
http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
For reproducing experimental data I would look in the original force-field
publications.
Oliver
On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts
Hi Yun,
Mixed 1-4 scaling of AMBER and GLYCAM requires a trick originally designed
for including berger lipids and the OPLS forcefield. I think* the original
idea came from Chris Neale and I think there is a paper in detailed in there
you should cite. It was recently explained on the GMX list how
It's reading it as GLY tho so maybe you have NGLY in the wrong column? Maybe
try move it over one to the right?
Oliver
On 24 August 2011 09:47, Kamesh Narasimhan wrote:
> The termini were changed to NXXX/CXXX and the aminoacids.dat file has
> these two names as well. So nothing very evident.
>
Hi SA,
I think this is due to the original amb2gmx.pl coder only considering AMBER
type dihedrals. He/She didn't expect any negative values. You'll notice
certain groups like NAc and COO- on sugars are affected when you run your
simulation. Below is a similar post with a fix to the amb2gmx.pl code
g_sgangle will do this for you. You're lucky your rings are planar ;)
Oliver
On 17 May 2011 16:34, wrote:
> 1. Determine some mathematical calculation that you want to apply to some
> atoms.
> 2. make a .ndx group that includes all of those atoms
> 3. Run g_traj -ox to output the coordinates of
This is review of all the carbohydrate force fields. It's only missing the
latest CHARM one which I think is available in the latest release of
gromacs.
E. Fadda and R.J. Woods, “*Molecular* *Simulations* of *Carbohydrates* and *
Protein-Carbohydrate* *Interactions*: *Motivation*, *Issues*, and *P
>From my own reading the Berger values are already scaled so to include them
in gromacs by themselves no scaling would be required (like fudge=1.0).
However OPLS 1-4 should be scaled by 0.5. So Chris Neale's method is to use
fudge = 0.5 for OPLS and include the berger values twice. Here is a summar
In the pdb, before pdb2gmx, rename the CYS residues involved in the S-S
bonds as CYS2.
If you don't know this then you need to read everything on this page about
using the amberports:
http://ffamber.cnsm.csulb.edu/
As you may have other issues with HIS and LYS residues.
Oliver
--
gmx-users mailin
Show us that part of your topology. When you used ffamberports have you
renamed the CYS to CYS2?
Oliver
On 20 January 2011 09:23, wrote:
> > Message: 5
> > Date: Wed, 19 Jan 2011 08:37:20 -0500
> > From: "Justin A. Lemkul"
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Disc
Hi all,
I currently mix GLYCAM and AMBER in gromacs4.0.7 using the amberports and
amb2gmx.pl for the glycan. My problem is that I can't mix the scaling
properly as required for correct rotamer population sampling of the glycan
with the protein present.
>From Glycam_06g.dat:
"Correct rotational be
Hi Xiaodu,
Yes I remember now I had the same problem. Copy the forcefield.itp to your
working directory and make the change there. Your working directory is
searched first. However as you will be including a protein in your
simulation you will need to have fudge set to 0.5 for 1-4 scaling with the
Hi Xiaodu,
The fudgeLJ under defaults should be 1.0 for GLYCAM. I'm unable to check my
own files right now so can't compare. When you run grompp check in the
output that fudge is set to 1.0. So there will be no protein in your
simulation correct? I think there is a way to do mixed scaling in groma
Hi,
Not sure exactly what you plan to simulate but here are a couple of
potential pitfalls:
Does acpype call amb2gmx.pl or is it new code that converts? If it is a
amb2gmx.pl call I'd check the torsions on the NAc group if you have one.
They didn't get translated when I used it.
When using amber
Hi Leila,
I would try the other suggested options like catdcd or vmd. The script is a
pain and you would have to adapt it to work with DNA. It cost me a lot of
time.
I used g_hbond for residence time like this:
g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num >
g_hbond.log
o get % residence,
average bond length and std dev of length but I had to use ndx files with
just the 3 atoms in them. It's tedious so if you have a lot of bonds check
out the perl script.
Oliver
On 7 December 2010 10:56, leila karami wrote:
> Dear Oliver Grant
>
> thanks for yo
I suppose it depends on what kind of analysis you would like to do... I'm
not aware of any scripts for converting back from gmx into amber
trajectories but I have done this before when doing an mmpbsa calculation
using ambertools. As I only needed "snaphots" of the trajectory and not
energies or ve
I would use grep and cut to take the atom numbers of the residues I want to
restrain and direct them into an index file with [res_sol] at the top. Then
use genrestr to generate restraints for these atoms using the -n option.
Then conditionally include this restraint file (.itp file) in my topology
You could use GLYCAM which is in AMBER so the parameters are already there
in the correct format (but not in the AMBER ported to GROMACS) and convert
that to GROMACS topology. It'll save you some time :)
I had problems converting the improper dihedral that holds the NAc group
planar using amb2gmx.p
Hi Carla,
I've seen this behavior too but I didn't look at the code. I figured with
the hydrogen included it checks the angle too or if the hydrogen is between
the two heavy atoms. So the first pass just looks at distances between donor
and acceptor atoms and doesn't consider that the hydrogen may
Hi Carla,
I did this using g_hbond by supplying an index file with only the 3 atoms
involved in the individual bond I was looking at.
I got this printed to screen:
"Average number of hbonds per timeframe 0.998 out of 1 possible"
Although it is time consuming to do it for more than a few hydroge
Hi,
This seems to be a problem with amber ports in gromacs. I believe it is
because the residue attached to an N terminal residue. Try manually adding
the hydrogen to the backbone nitrogen in the SER2 in the pdb. This solved
the problem for me although there were reports from other people of the
0ns, 1ns, 2ns and 3ns gives four files.
On 16 July 2010 10:47, sonali dhindwal wrote:
> Thanks Tsjerk,
> I was confused, that why 3 files are generated as output. I will check it.
> I appreciate what you said, I will read more.
> Regards
>
> --
> Sonali Dhindwal
>
>
> --- On *Fri, 16/7/10, Tsjer
Hi Abdul,
Could you post your pdb and your command line please? I'll take a look for
you. I think this is a bugzilla as mark suggested but maybe more
specifically an amber ports problem.
Oliver
On 6 July 2010 09:48, abdul wadood wrote:
> Dear gmx-usrs
>
> Thanks you all for you valuable sugge
Dear Abdul,
I had a similar error always with residue number 2 when using the amber
ports in gromacs. Manually adding the hydrogen to the backbone nitrogen that
connects to residue 1 will fix this.
You might know how to do this but just in case here is how I do it:
load your pdb into any builder
1. pdb2gmx, editconf and then solvate.
2. use trjconv and make a pdb.
3. Take 7 water molecules and put them in the top of your original pdb and
start again from there.
On 3 June 2010 09:34, NG HUI WEN wrote:
> Looks like I’ve got some work to do. Thanks Mark!
>
>
>
> *From:* gmx-users-boun..
You could use coot(or any builder). With coot mutate your SER into a SER
which will fill in your heavy atom gaps. Write out the pdb and either use it
or copy the atom into your original pdb. Guessing the position would work
fine too.
On 29 May 2010 01:12, Mark Abraham wrote:
> - Original Mes
*If you are familiar to ambertools (tleap mainly), so you can create your
molecule there, save the amber parameters and use acpype to convert from
amber to gromacs format.
*Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only
problem is the NAc groups aren't restrained properly s
t. Apologies for the
confusion!
Oliver
-Justin
On 20 May 2010 13:00, Justin A. Lemkul wrote:
>
>
> Oliver Grant wrote:
>
>> The force fields have to be compatible but this way works fine.
>>
>>
> I guess that depends on what you mean by "works fine."
The force fields have to be compatible but this way works fine.
On 19 May 2010 12:50, Justin A. Lemkul wrote:
>
>
> Oliver Grant wrote:
>
>> Can you not run pdb2gmx for each of your molecules that you want separate
>> force fields for? Then cat the gro files, renumber
Can you not run pdb2gmx for each of your molecules that you want separate
force fields for? Then cat the gro files, renumber and include the molecule
types as .itp files in the .top file as below. If I'm doing anything wrong
please let me know! :)
;
;This is your topology file
;"What If N
And at what time point does it explode? What minimization, equilibration
steps did you use?
On 13 May 2010 18:53, Giovana Bergamini wrote:
>
> Hi!
> We have a problem with a protein-ligand-protein simulation. It is a
> somewhat
> large system (approx. 360 amino acid residues with approx. 70
> mo
Command is xmgrace and it needs to be in your $PATH.
On 13 May 2010 12:19, shahid nayeem wrote:
> Dear all
> I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
> tar -xvzf xmgr-4.1.2.tar.gz
> cd xmgr-4.1.2
> ./configure
> make
> make install
> But it gives error command x
x27;d like the center of mass
removal to keep the sugar in the center.
Oliver
On 29 April 2010 12:40, Justin A. Lemkul wrote:
>
>
> Oliver Grant wrote:
>
>> Hi there,
>>
>> I'm running a 200ns simulation with a small trisaccharide in water. The
>> trisac
Hi there,
I'm running a 200ns simulation with a small trisaccharide in water. The
trisacc drifts around the box. I've tried using comm-grps = System and
comm-grps = and comm-grps = carb and what is below.
carb is the name I use in my top file and index file. For the index I
specify the groups in
You could load your gro and trr file into vmd, label the angle, save the
file and plot using excel.
Oly
On 28 April 2010 22:26, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Hello,
>> I am doing solvation of glucose. I am trying to calculate a angle between
>> three selected carbon at
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