Re: [gmx-users] CNT topology

[Justin A. Lemkul]

sara wrote:


Dear All Users
 
I am beginner to GROMACS. I want to simulate CNT in water. I made pdb 
file by VMD and then made .gro by "editconf -f file.pdb -o file.gro -box 
4" command. then for made topology file, I use .n2t itp, .itp, .rtp, 
ff.dat, and by "x2top -f file.gro -o topol.top -ff cnt_oplsaa -name CNT 
-noparam -pbc" command. it makes topology file. but when I want to add 
water by "genbox" it make "topology.top" but there is not the water 
parameters(there is only number of water molecules at the end of file).
then I use #include command for tip3p.itp model. when I want do em run 
by grompp, it dos not make .tpr and give error:

"Fatal error:
[ file tip3p,itp, Line 42 ]:
Atom index (1) in settles out of bounds (1-0).   ."


You've placed your #include statement in the wrong location.

http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds

I studied some guides to another gromacs user in mailing list and add 
"#define ff.." in ffcnt_oplsaa.itp but it gives this error again.


Without seeing the contents of your topology, no one can comment on whether or 
not this is appropriate.


I think because of  use ffcnt_oplsaa.itp , it can't include tip3p.itp. 


You can #include any series of legitimate .itp files.  In your case, you 
probably have something nested inside another [moleculetype].


-Justin


but when I add this forcefield to tip3p.itp by hand this error again comes.
please guide me.
thank you so much
Best
 
Sara Azhari

Phd Student




--


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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[gmx-users] CNT topology

[sara]

Dear All Users
 
I am beginner to GROMACS. I want to simulate CNT in water. I made pdb file by 
VMD and then made .gro by "editconf -f file.pdb -o file.gro -box 4" command. 
then for made topology file, I use .n2t itp, .itp, .rtp, ff.dat, and by "x2top 
-f file.gro -o topol.top -ff cnt_oplsaa -name CNT -noparam -pbc" command. it 
makes topology file. but when I want to add water by "genbox" it make 
"topology.top" but there is not the water parameters(there is only number of 
water molecules at the end of file). 
then I use #include command for tip3p.itp model. when I want do em run by 
grompp, it dos not make .tpr and give error:
"Fatal error:
[ file tip3p,itp, Line 42 ]:
Atom index (1) in settles out of bounds (1-0).   ."
I studied some guides to another gromacs user in mailing list and add "#define 
ff.." in ffcnt_oplsaa.itp but it gives this error again. 
I think because of  use ffcnt_oplsaa.itp , it can't include tip3p.itp. but when 
I add this forcefield to tip3p.itp by hand this error again comes. 
please guide me.
thank you so much
Best
 
Sara Azhari
Phd Student


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