All these parameters are for Mg2+, forgot to mention.
On Fri, May 31, 2013 at 10:48 PM, tarak karmakar wrote:
> Dear All,
>
> I have a little confusion with the non-bonding parameters conversion from
> OPLS-AA to CHARMM in gromacs.
> If I see the ffnonbonded.itp in both the cases I get the foll
On 2011-03-18 12.23, Cen-Feng Fu wrote:
Hi David,
Thanks for your suggestion. Now I have complete the topology files for
benzyl alcohol and phenylethanol.
However, I have a new doubt. In your topology file for benzyl alcohol,
; ring_180
1 3 5 7 1 180 4.6 2
3
Hi David,
Thanks for your suggestion. Now I have complete the topology files for
benzyl alcohol and phenylethanol.
However, I have a new doubt. In your topology file for benzyl alcohol,
; ring_180
1 3 5 7 1 180 4.6 2
3 5 7 9 1 180 4.6 2
5
you zou wrote:
Hi,
Thank you for your help.Now there is this question that I have just .pdb file
and when use protonate command it is" protonate -f drg.pdb -o drg.gro", this
is without hydrogens atoms too.
I think something is wrong, but I don't know what it is.In definition of
"protonate" th
Hi,Thank you for your help.Now there is this question that I have just .pdb
file and when use protonate command it is" protonate -f drg.pdb -o drg.gro",
this is without hydrogens atoms too.I think something is wrong, but I don't
know what it is.In definition of "protonate" there is "protonate r
you zou wrote:
Hi again,
Sorry, I have one question now, what is the meaning of structure? I think
coordinates is structure, is it true?
Yes, a coordinate file contains a structure.
If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms
are different from top file and
Hi again,Sorry, I have one question now, what is the meaning of structure? I
think coordinates is structure, is it true?If it is true, when I used "editconf
-f drg.pdb -o drg.gro" number of atoms are different from top file and editconf
can not add hydrogens to drg.gro. If Gromacs can handle .p
*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
Dear Oliver,
On Thu, May 20, 2010 at 13:21, wrote:
> I'm using GLYCAM06, so it involves a bit more effort to generate a .top and
> .gro file than just using pdb2gmx but I thought I'd leave it out as I just
> wanted to explain the method I use to include it. Apologies for the
> confusion!
>
If y
*I guess that depends on what you mean by "works fine." *
I mean the method of using pdb2gmx to generate a top and gro and then
appending the gro files and including the .itp files in the .top file, works
if you want to use two force fields. Originally I thought that was the
question.
*I guess i
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." If you mean that you can
produce a stable simulation, then yes, it may "work," but I would question the
underlying premise of combining different forc
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 and include the molecule
>>
you zou wrote:
Hi again,
Sorry I confused you with my question. My question is How can I make .gro
file and .top file from drug.pdb (that removed from drug-enzyme.pdb)?
If I can use x2top command I will make .top file just, is it true? I think
.gro file is dependent on forcefiled too so If I
Hi again, Sorry I confused you with my question. My question is How can I make
.gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I
can use x2top command I will make .top file just, is it true? I think .gro file
is dependent on forcefiled too so If I use editconf com
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 and include
the molecule types as .itp files in the .top file as below. If I'm doing
anything wrong please let me know! :)
Combining different for
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
you zou wrote:
Hi Justin,
Thank you for your help, But when I run x2top command there is one error
that is:
"
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207
Fatal err
Hi Justin,
Thank you for your help, But when I run x2top command there is one error that
is:"Can not find forcefield for atom C1-1 with 2 bondsCan not find forcefield
for atom C4-4 with 2 bonds...Program x2top, VERSION 4.0.5Source code file:
x2top.c, line: 207Fatal error:Could only find a force
Hi You Zou,
Complementing Justin's message, I would invite you to take a look at
acpype.googlecode.com. It's my attempt to address problems like yours.
There's also links to some options besides ACPYPE.
Bear in mind that you should know what you're doing. I would suggest you to
read the Wiki's th
Sebastian Kruggel wrote:
hi justin,
thanks for the quick answer and ...
> Either way, parameterization is going to be hard.
so you don't think the use of default parameters of gmx-ff as described
in the drug-enzyme-tutorial to be useful (to give reasonable results) if
i want to get an imp
hi justin,
thanks for the quick answer and ...
> Either way, parameterization is going to be hard.
so you don't think the use of default parameters of gmx-ff
as described in the drug-enzyme-tutorial to be useful (to
give reasonable results) if i want to get an impression of
the stability of
What hydrogen did you use? Without substantially more cut and paste on
your end I am in the dark and can't help very much.
On the side, I'll mention that your sigma, and especially your
epsilon, looks very low here. I'm no gold expert though, and I am just
pointing that out even though that
Here are some more details:
My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.
I could also add that each Ag belongs to its own charge group, so they
s
what's your minimum atomic distance achieved between Ag and your other molecule (g_mindist)?
If it's < 0.09 nm then you definitely do have some error in your setup. For
proof of that, generate a new system that is identical to yours
but this time use only standard OPLS atom-types and see the pr
Hi Chris,
I've done a gmxdump and there aren't any zeros for any of the LJ values.
No capital letter problems either.
Chris Rowan
Mon, 27 Jul 2009 12:30:54 -0700
Sounds like your topology/forcefield is incorrect or incomplete.
Does your log file from mdrun or the stderr/stdout from grompp/md
Dear all,
Thanks for the suggestions. I actually solved the problem myself, so
here's the solution:
OPLS has other N and C terminal patches, including 'ZWITTERION_NH3+' and
'ZWITTERION_COO-'. These are designed for exactly my situation and both
set the CA charge to the same value. In the cas
Hello,
I believe this question has been asked several times. It is true that
ffoplsaabon.itp misses some parameters for dihedral for the capped
residues (ACE NAC). I think you can add some estimated values to the
ffoplsaabon.itp, or ignore the warnings.
All the best!
Donnsheng
On Sat, 2006
Hi,
I have checked both the files. These lines corresponds to following
dihedrals in my topology
Dihedral (1-5-7-9)
1 opls_135 1ACECH3 1 -0.18 12.011 ; qtot
-0.18
5 opls_235 1ACE C 20.5 12.011 ; qtot
0.5
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