abdullah ahmed wrote:
Hi!
In your previous mail you mentioned:
The position restraints must belong to the [moleculetype] of
the species to be restrained. * Once you #include a new molecule, you
start a new
[moleculetype] entry and the position restraints belong to it. *
So I rechecked my .top file and found that [moleculetype] only occurs
once. Perhaps I have misunderstood you. So I added the top file below. I
No it doesn't. Each time you #include a new .itp file, you are telling grompp
to copy and paste the contents of that .itp file in that location. Have a look
at spc.itp - it starts a new moleculetype.
http://www.gromacs.org/Documentation/Include_File_Mechanism
Note how the automatically-generated "posre.itp" file is #included at the end of
the Protein_A moleculetype, *before* any other molecules are introduced. You
have to do the same with any new #include statements or directives you add.
-Justin
did not add the contents of [atoms] [bonds] etc because I felt the mail
would become unnecessarily long.
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein_A 3
[ atoms ]
[ bonds ]
[ pairs ]
[ angles ]
[ dihedrals ]
[ dihedrals ]
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_A 1
Thanks again for your help,
Abdullah
------------------------------------------------------------------------
Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign
up now. <https://signup.live.com/signup.aspx?id=60969>
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.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
