Just an update, I decided to create a new residue for an isolated GMP. Well,
not really, because I used pdb2gmx to output a topology of a dimer, and then
modified it carefully to extract the topology of a phosphorylated GTP.
thank you !
On Tue, Mar 22, 2011 at 2:52 PM, maria goranovic
wrote:
>
the gro file was the input. I am attaching a pdb as well
CRYST1100.0100.0100.0 90.00 90.00 90.00 P 1 1
ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00
P
ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00
O
ATOM 3 OP2 G A 4
maria goranovic wrote:
Sorry for the incomplete reply.
version 4.5.3,
command: pdb2gmx -f guan.pdb -ignh
I tried using -ter, but that did not help.
It appears that pdb2gmx is not equipped to handle the case of an isolated
nucleotide. Keep in mind that pdb2gmx is intended for use with re
Hi,
Is this your input? (a GRO file?). Can you paste the PDB corresponding to
the RNA nucleotide that you are interested on? I think the file may be small
enough to paste it here so someone can try to reproduce what is happening to
you.
Daniel
2011/3/22 maria goranovic
> Sorry for the incomple
Sorry for the incomplete reply.
version 4.5.3,
command: pdb2gmx -f guan.pdb -ignh
I tried using -ter, but that did not help.
input coordinate file, pulled out from an RNA molecule.
Gromacs Runs On Most of All Computer Systems
34
1GP1 5.549 4.916 5.071
1G OP1
On 22/03/2011 8:15 PM, maria goranovic wrote:
is this a bug of some kind then? someone ? anyone?
It's still hard to say. I asked you for your GROMACS version and input
coordinate file, and you didn't give us either (in full). While you're
there, what pdb2gmx command did you use?
Mark
just
is this a bug of some kind then? someone ? anyone?
just bumping,
maria
On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic
wrote:
> Here are the contents of my input coordinate file.
>
> CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1
> ATOM 1 P G A 4 5.48
Here are the contents of my input coordinate file.
CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1
ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00
P
ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00
O
ATOM 3 OP2 G A 4 5.367
On 19/03/11, maria goranovic wrote:
> Dear All
>
> I am trying to generate a topology for guanosine monophosphate: i.e. an RNA
> base with a phosphate at the 5' Carbon. I tried to read in a pdb file
> containing all atoms, and used pdb2gmx with CHARMM. However, the output
> coordinate file
Dear All
I am trying to generate a topology for guanosine monophosphate: i.e. an RNA
base with a phosphate at the 5' Carbon. I tried to read in a pdb file
containing all atoms, and used pdb2gmx with CHARMM. However, the output
coordinate file has no phosphate group on it. Why does the phosphate
di
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