1 1.1210.180.96 ; S
> SH 0.18 1 1.1210.180.96 ; S
>
> ; masscenters for vsites do not have gbsa parameters
>
> MNH3 00 00 0
> MCH3 00 00 0
>
>
>
> 8 n
ist and I'll take a look.
> I suspect the issue is that different radii are being used, as Gromacs
> does not use the Bondi radii.
>
> Cheers
> /Per
>
>
> 8 nov 2012 kl. 16:35 skrev Sandeep Somani:
>
> > Hi Per
> >
> > Pls see inline comments:
>
e creating amber prmtop files in leap. The difference in EGB
is just 2-3 kcal/mol .. not enough to bridge the gap.
Best
Sandeep
> Cheers
> /Per
>
>
> 8 nov 2012 kl. 05:43 skrev Sandeep Somani:
>
> > Hi,
> >
> > I am comparing single point amber ff energies fr
Hi,
I am comparing single point amber ff energies from gmx4.5.5 (double
precision) and Amber11.
All bonded and non-bonded energy terms are in very good agreement (within
0.1 kJ/mol) except GB:
gmx 'GB polarization' = -200 kJ/mol
amber 11 'EGB' = -283 kJ/mol.
I am basically trying to re
nal pdb==
On Fri, Sep 9, 2011 at 11:35 AM, Mark Abraham wrote:
>
>
> On 09/09/11, *Sandeep Somani * wrote:
>
> Hi Mark
>
> Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and
> renamed residue and atom names in pdb file.
DIAL*
*ATOM 32 HT3 CT3 2 8.048 1.201 -0.907 1.00 0.00
DIAL*
TER 33 CT3 2
END
modified pdb=
On Fri, Sep 9, 2011 at 2:52 AM, Mark Abraham wrote:
> On 9/09/2011 8:05 AM, Sandeep Somani wrote:
>
>> H
Hi
I am trying to set up a simulation for dialanine using charmm27 ff but am
getting errors in pdb2gmx due to missing definitions in rtp file.
I created the pdb file (below) using Charmm for the sequence
ACE-ALA-ALA-CT3.
pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and
C
Hi
I am trying to extract bond lengths and bond angles from a trajectory file
using g_bond and g_angle.
Original simulation generated a xtc file which I then converted to pdb using
trjconv.
Turns out that for some frames bond lengths (and angles) computed using the
xtc file are different from tha
ok, just realized that -ov option of g_angle gives the values for each
frame.
ignore my previous mail.
Rgds
Sandeep
On Sat, Sep 26, 2009 at 6:32 PM, sandeep somani wrote:
> Hi Justin
>
> I had missed the -type flag of g_angle.
>
> But it gives the distribution of the dihedral
@ xaxis tick minor 30
@ yaxis tick major 0.005
@ yaxis tick minor 0.0025
-180 0.035465
-179 0.032967
:
:
I guess it should be easy to modify the code to get the value out for each
frame.
Thanks
Sandeep
On Sat, Sep 26, 2009 at 5:54 PM, Justin A. Lemkul wrote:
>
>
> sandeep som
hi
I have simulated a molecule (not a standard protein) with gmx and now need
to compute dihedral angles between specified atoms for all frames of in the
.xtc file.
Is there any utility along the lines of g_bond whcih computes the
dihedral/torsion angle given 4 atom numbers in a index file group
i see. i reran the trajectory with reaction field electrostatics and that
gave a more negative energy value which was closer to what i was expecting.
i guess the missing reciprocal space contributions explains this
discrepancy.
is there a way to get the full interaction energy with PME ?
thnx fo
Hi All
I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
for 400 ps and extracted the interaction energy of a randomly picked water
molecule with rest of the system.
Simulation was done at 298K and 1bar and usual procedure for generating a
water box and equilibration were
:14 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Cannot allocate memory" by grompp
Sandeep Somani wrote:
> Hi
>
> I am testing a fresh gmx3.3 installation on a new dual opteron cluster
> running redhat linux.
>
> Did the standard pdb2gmx ->
Hi
I am testing a fresh gmx3.3 installation on a new dual opteron cluster
running redhat linux.
Did the standard pdb2gmx -> energy minimization -> position restrained (PR)
MD and everything was fine.
But next when I did grompp for production run, got the following:
"
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