Yi Gao wrote:
Hi, Justin,
Thanks for your advice! Do I need to add this part:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
This section is only necessary if you want to restrain the water molecules.
; Include generic topology for ions
#include "ions.itp"
This section is only necessary if you will be using ions described ions.itp.
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
SOL 216
Whether or not these directives are correct for your system is something only
you can determine. I would encourage you to do some basic tutorial material and
reading in Chapter 5 of the manual to understand all of these sections.
-Justin
Thanks a lot!
Yi
On Sat, Sep 4, 2010 at 11:21 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Yi Gao wrote:
Hi, I used x2top to generate spc216.top. The spc216.gro file
comes from Gromacs tutor directory. I use Gromacs 4.0.5 version.
The command line is x2top -f scp216.gro -o scp216.top. The error
message is
Can not find forcefield for atom OW-1 with 2 bonds
Can not find forcefield for atom OW-4 with 2 bonds
Can not find forcefield for atom OW-7 with 2 bonds
Can not find forcefield for atom OW-10 with 2 bonds
Can not find forcefield for atom OW-13 with 2 bonds
Can not find forcefield for atom OW-16 with 2 bonds
Can not find forcefield for atom OW-19 with 2 bonds
Can not find forcefield for atom OW-22 with 2 bonds
Can not find forcefield for atom OW-25 with 2 bonds
Can not find forcefield for atom OW-28 with 2 bonds
Can not find forcefield for atom OW-31 with 2 bonds
Can not find forcefield for atom OW-34 with 2 bonds
Can not find forcefield for atom OW-37 with 2 bonds
...
-------------------------------------------------------
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207
Fatal error:
Could only find a forcefield type for 432 out of 648 atoms
-------------------------------------------------------
I don't want to use pdb2gmx to generate *.top file, because
spc216 water is just a part of my system. Could anyone help me
to resolve this problem? Thanks a lot!
There is no need to do any of this. Just #include "spc.itp" in your
topology. See the manual for details, as well as:
http://www.gromacs.org/Documentation/Include_File_Mechanism
-Justin
Best,
Yi
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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]>
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]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
