Hi Subarna,
There is no .dat format for topologies. It may be named .dat, but the
inside (format) is what matters. If you're confident it is gromos96
format, you can #include it the same way as other molecule definition
topology files. Do mind that there's quite a difference between
GROMOS96 43a1,
Hello
I have a gromos96 topology file for a ligand and it is in xx.dat format.How do
I include this file in my gromacs version 4.0 simulation of a protein?
Subarna
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gmx-users mailing listgmx-
radhika jaswal wrote:
Respected Sir,
Please tell me how to simulate two different stuctures together in a
water box so as to have an idea of drug docking and what options to use.
Any suggestions are welcome.
Your question is too general. If you need help with GROMACS workflows,
you should ex
pawan raghav wrote:
After installing gromacs4.0 on windows it created Gromacs directory
containing several .exe files in bin directory. But when I used pdb2gmx
command it will shows that basch command is not found. So anyone can
tell me what is that.
See point 8 here
http://www.gromacs.org
After installing gromacs4.0 on windows it created Gromacs directory
containing several .exe files in bin directory. But when I used pdb2gmx
command it will shows that basch command is not found. So anyone can tell me
what is that.
--
Pawan Kumar Raghav
Bioinformatician
Stem Cell and Gene Therapy
Respected Sir,
Please tell me how to simulate two different stuctures together in a
water box so as to have an idea of drug docking and what options to
use. Any suggestions are welcome.
With Regards
Radhika
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h
Thanks Justin! Got it now.
On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul wrote:
>
>
> Jack Shultz wrote:
>>
>> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul wrote:
>>>
>>> Jack Shultz wrote:
>>>
>>>
>>>
---
Program pdb2gmx, VE
Jack Shultz wrote:
On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul wrote:
Jack Shultz wrote:
---
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom O in residue CARG 244 not found in rtp entry with
On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul wrote:
>
>
> Jack Shultz wrote:
>
>
>
>> ---
>> Program pdb2gmx, VERSION 4.0.5
>> Source code file: pdb2gmx.c, line: 429
>>
>> Fatal error:
>> Atom O in residue CARG 244 not found in rtp entry wit
Jack Shultz wrote:
---
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom O in residue CARG 244 not found in rtp entry with 25 atoms
while sorting atoms
Jack Shultz wrote:
I modified the N-Terminal and C-Terminal Residues.
[boinc...@vps test]$ grep NGLU ProteinAmber.pdb && grep CARG ProteinAmber.pdb
ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00
N
ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00
I modified the N-Terminal and C-Terminal Residues.
[boinc...@vps test]$ grep NGLU ProteinAmber.pdb && grep CARG ProteinAmber.pdb
ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00
N
ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00
C
ATOM 3 C NG
Can you be more specific in the question of what property you want to
compute for which molecule or molecules? Linear Interaction energy
approaches are not always very efficient for coulomb, and is
definitely not exact for the LJ term. So LIE might not be what you
want to be doing.
Michael Shirts
Jack Shultz wrote:
Well I was just wondering if there was some porgram that could add
this atom automatically. It looks like this "H" is missing. I supposed
I could re-write the pdb file. It has all these non-standard
Hydrogens. HB, HG and HT. Maybe I can just replace those.
Non-standard? H[ABG
Jack Shultz wrote:
I tried to protonate my pdb file using openbabel
babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h
Then I ran pdb2gmx with the following
pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p
Protein.top -water spce -ignh
But apparently I am missing a H from my f
Well I was just wondering if there was some porgram that could add
this atom automatically. It looks like this "H" is missing. I supposed
I could re-write the pdb file. It has all these non-standard
Hydrogens. HB, HG and HT. Maybe I can just replace those.
This is the residue in question
ATOM
Jack Shultz wrote:
I tried to protonate my pdb file using openbabel
babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h
Then I ran pdb2gmx with the following
pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p
Protein.top -water spce -ignh
But apparently I am missing a H from my fir
I tried to protonate my pdb file using openbabel
babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h
Then I ran pdb2gmx with the following
pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p
Protein.top -water spce -ignh
But apparently I am missing a H from my first residue. Is there
Hi,
VMD was built to work with NAMD, so the atom names and topologies will not
work with GROMACS. I guess you better go to Peter Tieleman site (
http://moose.bio.ucalgary.ca/) and rad there how to do things.
Cheers,
Itamar
On Tue, Nov 10, 2009 at 8:05 AM, Mark Abraham wrote:
> parthi...@ncbs.re
parthi...@ncbs.res.in wrote:
Hi
I have constructed the bilayer with protein molecule in VMD.
Can any one tell how to start MD from here.
Follow the methods of whichever tutorial you learned from :-)
the initial step - pdb2gmx is not working for this complex(pdb+membrane)
We're not omnisci
Ramachandran G wrote:
I commented out the 'read_next_x' routine and in place of it i added
'read_next_frame' as given below will that work?
You could try it, but it won't work. The whole do...while loop needs to
be adjusted to use fr and its struct members, rather than separate box,
t, x, et
It works.
Thank you so much.
Regards,
Gunnar W.
On Mon, Nov 9, 2009 at 4:26 PM, Bruce D. Ray wrote:
> On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson
> wrote:
>
> > Thank you.
> > I am new to Unix commands, so could you please explain a little more how
> I am to
> > apply th
Hi
I have constructed the bilayer with protein molecule in VMD.
Can any one tell how to start MD from here.
the initial step - pdb2gmx is not working for this complex(pdb+membrane)
thanks in advance
Parthiban
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http://lists.gromacs.org/mailman
I commented out the 'read_next_x' routine and in place of it i added
'read_next_frame' as given below will that work?
Now if i install will i get the trajectory? Is API available for
gromacs? Thank you.
write_trx(out,natoms,swi,&top.atoms,0,t,box,x,NULL);
}
/* } while(read_next_x(status,
I'm interesting to calculate Gibbs energy using g_lie application.
Unfourtunately, I don't know what kind of state equation is the
sub-program using. Can you help me with that.
Best regards
Jorge R. Quintero
Grupo de Investigación en Fisicoquímica Teórica y Experimental
Universidad Industrial
On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson
wrote:
> Thank you.
> I am new to Unix commands, so could you please explain a little more how I am
> to
> apply these bug fixes?
For short patches like these, I just use a text editor.
Because the mailing list does not like th
Thanks allot for the ultrafast response and above all your help !.
Arik
Mark Abraham wrote:
Arik Cohen wrote:
Hi,
Is there a way to tell the g_energy program the output option(i.e.
Potential, Temperature ) in advance when you run the program.
Namely, I would like to know if there is a
Thank you.
I am new to Unix commands, so could you please explain a little more how I
am to apply these bug fixes?
Thanks
On Mon, Nov 9, 2009 at 12:51 PM, Bruce D. Ray wrote:
> On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson
> wrote:
>
>
> > I have a small organic molecule t
Darrell Koskinen wrote:
Hi,
I am trying to create a topology file from a .gro file. When I run x2top
with methane (C4 opls_066) in my .gro file, I receive the following
warning:
/Can not find forcefield for atom C4-1 with 0 bonds/
I have included the following line in the ffoplsaa.n2t file,
On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson
wrote:
> I have a small organic molecule that I processed with antechamber
using the gaff forcefield
> and got a mol2 file. I want to get .gro and.
itp files from this to use with GROMACS. So I tried
> to use the program
"topolbui
Francesco Pietra wrote:
Does the atom2cg_v2.1.awk require the indication of the subunit (A, B,
C, etc) in the pdb file of a multimeric protein?
From
ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.0
Does the atom2cg_v2.1.awk require the indication of the subunit (A, B,
C, etc) in the pdb file of a multimeric protein?
From
ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C
ATOM 3 C
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