Hello Friends,I am new to gromacs. I configure the gromacs than it did not give
me error but when i run make command that it gave me following error.mpicc -O6
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops
-I/usr/include/libxml2 -o grompp topio.o toppush.o topcat.o
Hi Mark,
Thanks again, But I am Indian...will either of those flavour work for me
:-)
B.Nataraj
On Fri, 01 Dec 2006 16:21:59 +1100, "Mark Abraham"
<[EMAIL PROTECTED]> said:
> raja wrote:
> > Hi Goette,
> > Thanks for your mail. I have just find an article done a similar
> > work...I am trying to
Hi nr,
Thanks for your mail. Yea, I am looking for parameters like you
mentioned than partial charges.
B.Nataraj
On Thu, 30 Nov 2006 09:40:03 -0800, "Nathan C. Rockwell"
<[EMAIL PROTECTED]> said:
> Hydroxamates are also a bit tricky chemically; their chemistry is
> different
> than carboxylate
Hi Florian,
Thanks for your mail and introducing me the Antechamber site. I am
trying out there in that site.
B.Nataraj
On Thu, 30 Nov 2006 16:00:39 +0100, "Florian Haberl"
<[EMAIL PROTECTED]> said:
> hi,
>
> On Thursday 30 November 2006 13:01, raja wrote:
> > Dear gmxions,
> > I am writing a to
raja wrote:
Hi Goette,
Thanks for your mail. I have just find an article done a similar
work...I am trying to reach them to get their parameters. Unfortunately
I am not having Gaussian. Can you suggest me some other freely available
quantum mechanics software ?
GAMESS should get the job done. I
Hi Goette,
Thanks for your mail. I have just find an article done a similar
work...I am trying to reach them to get their parameters. Unfortunately
I am not having Gaussian. Can you suggest me some other freely available
quantum mechanics software ?
This reference article : "Binding affinity of hy
Hi,
Thank you for the response. Being that Fortran is much more my
language of choice than C, I was wondering if someone could point me in the
right direction as far as modifying the C code to do what I want. It is my
understanding that an mdrun begins by making a neighbor list, computing th
mario ciappy wrote:
Hello everyone,
when I try to minimise peptide-DPC system with grompp command, I find
the error
"Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891
Curiously enough, the error message:
Fatal error:
moleculetype DPC is redefined.
means that your .top
Hydroxamates are also a bit tricky chemically; their chemistry is
different
than carboxylates or amides, so parameters for the ASP or ASN side
chains
are unlikely to work. There are also some really old papers from
Gilchrist &
Jencks on alpha-effect nucleophiles that are good examples of why
hydrox
David van der Spoel a écrit :
Stéphane Téletchéa wrote:
editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc
But unfortunately, some lipids are not imaged (at least 18, 25 and
53). I tried using trjconv but it needs a topol.tpr that i don't have :-(
Any hint ?
Stéphane
It requires some manual w
Hello everyone,
when I try to minimise peptide-DPC system with grompp command, I find the error
"Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891
Fatal error:
moleculetype DPC is redefined.
I produced the dpc.itp file with dundee server.
Can you help me?
Thanks in advance.
hi,
On Thursday 30 November 2006 13:01, raja wrote:
> Dear gmxions,
> I am writing a topology for a ligand using AMBER99 force field
> convention. The ligand contains the hydroxamate group, for your quick
> reference I have drawn it below
>
>O
> HO||
>\ / \
> N
>
> Please le
Hi all,
hope you could help me with the following two issues :
First, after having introduced a new residue and used ffG43a1, I
produced a .top file. In the [pairs] section it is not supposed to
contain the 1-4 interactions since nrexcl=3, but surprisingly enough it
does! Why's that ? Is ther
Maybe, one could also think about calculating the RESP charges via QM,
e.g. with Gaussian...Further parameters, like force-constants and
dihedrals could also be evaluated...
But what's against an expensive random number generator?
I fear I'm doing this with FEP all day long...;)
Raja: We are (
Thanks Mark for your reply. And sorry about missing one hydrogen in my
drawn topology...
B.Nataraj
On Thu, 30 Nov 2006 23:12:10 +1100, "Mark Abraham"
<[EMAIL PROTECTED]> said:
> raja wrote:
> > Dear gmxions,
> > I am writing a topology for a ligand using AMBER99 force field
> > convention. Th
raja wrote:
Dear gmxions,
I am writing a topology for a ligand using AMBER99 force field
convention. The ligand contains the hydroxamate group, for your quick
reference I have drawn it below
O
HO||
\ / \
N
Your N has an unsatisfied valence... what's missing? (Don't bothe
Dear gmxions,
I am writing a topology for a ligand using AMBER99 force field
convention. The ligand contains the hydroxamate group, for your quick
reference I have drawn it below
O
HO||
\ / \
N
Please let me know which atoms type in amber can be used for these
atoms Espe
Stéphane Téletchéa wrote:
David van der Spoel a écrit :
Stéphane Téletchéa wrote:
Hello,
I'm willing to simulate a membrane protein, and to gain lipid
equilibration time, i'm using either Dr Tieleman's lipids or Dr
Vattulainen's lipids (dppc 128 / dppc64).
In order to fully surround my pro
David van der Spoel a écrit :
Stéphane Téletchéa wrote:
Hello,
I'm willing to simulate a membrane protein, and to gain lipid
equilibration time, i'm using either Dr Tieleman's lipids or Dr
Vattulainen's lipids (dppc 128 / dppc64).
In order to fully surround my protein, i need to enlarge tho
Stéphane Téletchéa wrote:
Hello,
I'm willing to simulate a membrane protein, and to gain lipid
equilibration time, i'm using either Dr Tieleman's lipids or Dr
Vattulainen's lipids (dppc 128 / dppc64).
In order to fully surround my protein, i need to enlarge those boxes to
get at least 256 l
Hello,
I'm willing to simulate a membrane protein, and to gain lipid
equilibration time, i'm using either Dr Tieleman's lipids or Dr
Vattulainen's lipids (dppc 128 / dppc64).
In order to fully surround my protein, i need to enlarge those boxes to
get at least 256 lipids (thus multiply the 64
Ok, I've got this paper and also the original (I hope
so) paper describing the method:
J Comput Chem. 2004 Mar;25(4):479-99.
Gallicchio E, Levy RM.AGBNP: an analytic implicit
solvent model suitable for molecular dynamics
simulations and high-resolution modeling.
The method is not very easy to
David van der Spoel wrote:
> so what's the reference for that?
>
> it's definitely not in vanilla gromacs, so I propose contacting the
> groningen group about it.
*Chemical Theory and Computation Special Feature: Comparative study of
generalized Born models: Protein dynamics*
Hao Fan, Alan E. M
Semen Esilevsky wrote:
Yes, that is exactly what I was asking about!
--- Ran Friedman <[EMAIL PROTECTED]> wrote:
There was a paper from the Groningen group with
Barry Honig about
implicit solvent simulations, where several GB
models were implemented
in Gromacs. Are those available?
so wh
Yes, that is exactly what I was asking about!
--- Ran Friedman <[EMAIL PROTECTED]> wrote:
> There was a paper from the Groningen group with
> Barry Honig about
> implicit solvent simulations, where several GB
> models were implemented
> in Gromacs. Are those available?
>
> David van der Spoel wr
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