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
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
*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
*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
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
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