[gmx-users] grompp error on nanotube
jackyxh at 163.com
jackyxh at 163.com
Sat Apr 15 05:56:13 CEST 2006
Hi,GMX group and other users:
I am a new user of gromacs(version 3.3). I want to do carbon nanotube MD.
When I run grompp, she told me that something must be wrong.
I am still very confused though I checked many of the "Mailing lists". So I type this for help.
I will tell what I have done in details, may anyone could give me a suggestion.
----------------------
1. Creat a "005.pdb" like this (though I don't know if the first 2 lines are necessary):
----------------------------
CRYST1 15 15 85 90.00 90.00 90.00 P 1 1
MODEL 1
HETATM 1 C1 UNK 1 3.390 0.000 0.000 1.00 0.00
HETATM 2 C10 UNK 1 2.268 -2.519 0.000 1.00 0.00
HETATM 3 0C10 UNK 1 0.354 -3.371 11.068 1.00 0.00
HETATM 4 1C10 UNK 1 3.390 0.000 12.298 1.00 0.00
HETATM 5 2C10 UNK 1 3.097 1.379 12.298 1.00 0.00
HETATM 6 3C10 UNK 1 1.048 3.224 12.298 1.00 0.00
HETATM 7 4C10 UNK 1 -0.354 3.371 12.298 1.00 0.00
HETATM 8 5C10 UNK 1 -2.743 1.993 12.298 1.00 0.00
HETATM 9 6C10 UNK 1 -3.316 0.705 12.298 1.00 0.00
HETATM 10 7C10 UNK 1 -2.743 -1.993 12.298 1.00 0.00
HETATM 11 8C10 UNK 1 -1.695 -2.936 12.298 1.00 0.00
HETATM 12 9C10 UNK 1 1.048 -3.224 12.298 1.00 0.00
HETATM 13 C11 UNK 1 2.743 1.993 1.230 1.00 0.00
HETATM 14 0C11 UNK 1 2.268 -2.519 12.298 1.00 0.00
.
.
HETATM 699 C98 UNK 1 -3.097 -1.379 11.068 1.00 0.00
HETATM 700 C99 UNK 1 -1.048 -3.224 11.068 1.00 0.00
.
.
CONECT 700 3 691 11
END
---------------------------
2. run >x2top -f 005.pdb -o 005.top -r cnt.rtp
But x2top did not creat a .rtp. I do not know what's the matter.
005.top is like this:
---------------------------------
; This is your include topology file
; Generated by x2top
;
; Include forcefield parameters
#include "ffgmx.itp"
[ moleculetype ]
; Name nrexcl
ICE 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 C3 1 UNK C1 0 0 12 C3 0 0 ; qtot 0
2 C3 1 UNK C10 1 0 12 C3 0 0 ; qtot 0
3 C 1 UNK C100 2 0 12 C 0 0 ; qtot 0
4 C 1 UNK C101 3 0 12 C 0 0 ; qtot 0
5 C 1 UNK C102 4 0 12 C 0 0 ; qtot 0
6 C 1 UNK C103 5 0 12 C 0 0 ; qtot 0
7 C 1 UNK C104 6 0 12 C 0 0 ; qtot 0
8 C 1 UNK C105 7 0 12 C 0 0 ; qtot 0
9 C 1 UNK C106 8 0 12 C 0 0 ; qtot 0
.
.
.
699 C 1 UNK C98 698 0 12 C 0 0 ; qtot 0
700 C 1 UNK C99 699 0 12 C 0 0 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 112 1
1 113 1
.
.
696 697 1
698 699 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 2 1
.
.
697 698 1
699 700 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
112 1 113 1
.
.
3 700 11 1
3 700 691 1
11 700 691 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
113 1 112 13 1
.
.
.
7 696 697 8 1
9 698 699 10 1
[ system ]
; Name
ICE
[ molecules ]
; Compound #mols
ICE 1
---------------------------------------------------
3. I also write a 005.gro file myself by changing the .pdb file. It's like this:
-------------
CNT005005_35!
700
1UNK C1 1 0.339 0 0
1UNK C10 2 0.2268 -0.2519 0
1UNK 0C10 3 0.0354 -0.3371 1.1068
.
.
.
1UNK C98 699 -0.3097 -0.1379 1.1068
1UNK C99 700 -0.1048 -0.3224 1.1068
15 15 85
-------------
4. Made a grompp.mdp file by changing a Gromacs tutor "nmr1.mdp"
--------------
5.run >grompp -f grompp.mdp -c 005.pdb -p 005.top -o topol
----------------
6 grompp tells the error:
-------------
creating statusfile for 1 node...
WARNING 1 [file grompp.mdp, line unknown]:
Unknown left-hand 'bd-temp' in parameter file
WARNING 2 [file grompp.mdp, line unknown]:
Unknown left-hand 'zero-temp_time' in parameter file
checking input for internal consistency...
calling /usr/bin/cpp...
cpp: too many input files
cpp exit code: 256
-I/usr/share/gromacs/top out.top > grompp4YaaUM'
The '/usr/bin/cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: grompp.c, line: 427
Fatal error:
number of coordinates in coordinate file (005005_35_2.pdb, 700)
does not match topology (out.top, 0)
==========================================================================
>grompp -f grompp.mdp -c 005.gro -p 005.top -o topol
shows the similar error message!
--------------------------------------------
What I have done is not valid, or where should I make a change?
(I think something must be wrong with the .top (not with cpp), but what is that? )
I have read hundreds of posts here, but still no idea with the "error"
can any one help me over this issue.
Thanking you
Jacky Allon
jackyxh at 163.com
--
If you send me one, I will always Re you three, friendship, help or anything else except emails and money:) ――Jacky Allon
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