He, Yang wrote:
Hello Justin,
Thank you for your reply. I am using the gromacs to simulate a case about the
course grain for DNA. This case includes some superatoms in the course grain
force field and I have defined the superatoms in the .atp files and the atoms
type in the water like this:
Ab 134.1; Adenine base of DNA
Tb 125.1; Thymine base of DNA
S 83.11; Sugar of DNA
P 94.97; Phosphate of DNA
OW 15.99940; water oxygen in SOL
HW 1.00800; water hydrogen in SOL
But it shows that Fatal error:
Atomtype 'OW' not found!
Also, this is my spc.itp file
[ moleculetype ]
; molname nrexcl
SOL 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
#ifdef _FF_GROMACS
1 OW 1 SOL OW 1 -0.82
2 HW 1 SOL HW1 1 0.41
3 HW 1 SOL HW2 1 0.41
#endif
#ifdef _FF_GROMOS96
#ifdef HEAVY_H
1 OW 1 SOL OW 1 -0.82 9.95140
2 H 1 SOL HW1 1 0.41 4.03200
3 H 1 SOL HW2 1 0.41 4.03200
#else
1 OW 1 SOL OW 1 -0.82 15.99940
2 H 1 SOL HW1 1 0.41 1.00800
3 H 1 SOL HW2 1 0.41 1.00800
#endif
#endif
#ifdef _FF_OPLS
1 opls_116 1 SOL OW 1 -0.82
2 opls_117 1 SOL HW1 1 0.41
3 opls_117 1 SOL HW2 1 0.41
#endif
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
Can you help me solve this problem
Well, what's in your *nb.itp file? You're obviously not using any of the force
fields that are called in the spc.itp file, so grompp doesn't know how to treat
OW in your force field.
-Justin
Thank you for your favor.
Regards,
Yang
________________________________________
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Tuesday, October 14, 2008 12:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs
He, Yang wrote:
Hi all users,
I juse encountered a problem when I run the code about the course grain for DNA,
it shows like this
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling cpp...
In file included from ffyxh.itp:8,
from hust.top:11:
ffyxhnb.itp:25:61: warning: no newline at end of file
In file included from ffyxh.itp:9,
from hust.top:11:
ffyxhbon.itp:26:5: warning: no newline at end of file
In file included from hust.top:65:
ffyxh.atp:6:34: warning: no newline at end of file
hust.top:76:17: warning: no newline at end of file
processing topology...
Generated 32 of the 36 non-bonded parameter combinations
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toputil.c, line: 61
Fatal error:
Atomtype 'OW' not found!
I have tried to solve that , but it did not still work . So anyone of you can
tell me how to solve that.
Well, what have you done to solve it? From the messages grompp is printing out,
it looks like the format of your files is badly mangled. You're calling
parameters for an atomtype which does not exist within the force field you've
apparently created. Parameters need to be defined within the .atp, *bon.itp,
and *nb.itp files for it to be recognized.
-Justin
Thank you in advance.
Yang
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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