[gmx-users] gromacs

[He, Yang]

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

Thank you for your favor.

Regards,

Yang

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

--
========================================

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

========================================
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.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 gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php