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" there is "protonate reads (a) conformation(s) and adds all
missing hydrogens as defined in ffgmx2.hdb
<http://rocks5.vki.ac.be/gromacs/online/hdb.html>." but I can't add
hydrogens. What is my problem?
Well, your command isn't correct. The protonate command takes (at minimum) the
-s flag, not -f (which is optional, and context-dependent, if I recall).
The other fact is that if a residue isn't listed in ffgmx2.hdb, it won't get
protonated, but it is trivial to add new molecules into the .hdb file with the
help of the manual. The syntax for .hdb entries is straightforward.
-Justin
Thanks
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 editconf can not add hydrogens to drg.gro.
If Gromacs can handle .pdb, How can it do this, because number of atoms are
different(Which command I have to use?). If can't handle it how can I add
Hydrogens to drg.gro?
The underlying assumption when running any simulation is that you have
developed the proper parameters for the ligand and that it has an appropriate
structure. If you need additional hydrogens, the Gromacs "protonate" tool can
generate an all-atom structure.
-Justin
Thanks,
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 use editconf
command I will miss something, is it true?
If you want to use x2top, the assumption is that the structure is already
appropriate as is, that is it is properly protonated. The only tool that is
smart enough to add force field-specific hydrogens is pdb2gmx. If you're
using OPLS-AA, then you should have all hydrogens present, anyway. If that's
true, then you can use editconf to create a .gro file (which is not
absolutely necessary; Gromacs can handle .pdb files just fine). If you
don't have all the appropriate atoms present in your molecule's structure,
then you need to build a proper structure.
-Justin
Thank you again
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 ...
&g t; Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207
Fatal error: Could only find a f
orcefield type for 6 out of 24 atoms"
Not all of your atom types are described by ffop
lsaa.n2t so you will have
to add them. There are only a limited number of types that are covered by
default.
http://www.gromacs.org/Documentation/File_Formats/.n2t_File
I don't know how
can I adjust this error. I have one more question again,
this command give me a top file, if I want gro file of this pdb (drug
that has removed from drug-enzyme complex) how can I do that?
Do you just need a .gro file, and not a .top? My understanding from your
first message was that you needed a topo logy. If you just need a .gro,
then simply pass your .pdb file to editconf.
-Justin<
br>>>
you zou wrote:
Dear Users,
I have one question about Drug-Enzyme Complex,Similar to tutorial If
I
want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
Beta version" server too, or not?
No. You can't use two different force fields in
one simulation system.
If I can't use this server, how can I make .gro file and .itp file
for
& gt;>> drug that remove from initial .pdb file?
There are several programs in the User Contributions from the website,
x2top (which is distributed with Gromacs), or you c
an build the topology
by hand. No matter what you choose, you ne
ed a thorough understanding of the mechanics of
your chosen force field, methods of validation, and of course Chapter 5
in the
Gromacs manual.
------------------------------------------------------------------------ Your
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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