Molecular Dynamics wrote:
Dear Justin,
I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the
PRODRG. And you suggested that ' If these come from PRODRG, they will
probably require manual modification and validation of their contents.'
What kind of modifications should I do ? Could you please give me some
1. If you are using the original PRODRG, don't. The parameters it generates are
for ffgmx, which is deprecated and should not be used. Use PRODRG-2.5 (beta
server) and get a Gromos96 43a1-compatible topology.
2. The charges and charge groups assigned by PRODRG are inconsistent, at best.
You will need to consult the manual for information about charge groups, and
existing elements of the force field to determine whether or not the charges
assigned are appropriate.
info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y
: 60 molecules number for example ) . According to your suggestions I
will have used DRGGMX.ITP and DRGPOH.PDB files of X molecule, but I
will just have used DRGGMX.ITP file of Y molecule. Isn't it important to
use DRGPOH.PDB file of Y molecule. Because Y is not a solvent. X and Y
I'm not sure I fully understand. You will obviously have to re-name the files
to have them make any sense. You also cannot call both of them "DRG" within the
.pdb and .itp files, as is the output of PRODRG.
are organic molecules. And I think this is the unique way to obtain a
binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could
you explain these significant issues ?
Using genbox should be fine.
-Justin
Sincerely
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Friday, March 13, 2009 8:25:14 PM
*Subject:* Re: [gmx-users] using more than one type of molecules
Molecular Dynamics wrote:
>
>
> Dear All,
>
>
> I'm new to Gromacs and have some questions to learn the answers. I
study on one type molecule. If I want to add lets say 240 molecules,
which is the best way to use editconf or genbox ? And I learned the
procedure of using more than one type of molecules in gromacs. But I'm
not sure, so I'm waiting for your contributions. Assume that I have two
small organic
In general, the topol.top should consist of the #include statements for
each .itp file, then the [ system ] directive should contain a count of
each molecule.
Use editconf to set your box size, and genbox -ci -nmol to insert what
you need.
> molecules like hydrocarbons X and Y. I think First I will have to get
seperately DRGGMX.ITP and DRGPOH.PDB for the each molecules in different
If these come from PRODRG, they will probably require manual
modification and validation of their contents.
> work directories. Then chose one directory ( X ) and do the
operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then
in this command
>
>
> genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top
>
>
If you are using X as the solute and Y as the solvent, then yes, this is
fine. It is just like solvating a protein in water (if X = protein, Y =
water).
> After I get gmx.pdb gmx.top files I will add #include “Y.itp” and
editing the number of Y molecule and go on ..
>
Correct.
-Justin
>
> Could you please help me to learn the true process of using more than
one type of molecules in gromacs ?
>
>
>
> Sincerely
>
>
>
> ------------------------------------------------------------------------
>
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
