[gmx-users] Atomtype CCL4 not found

[ahmet yıldırım]

Thanks Justin. Problem is solved.

.itp file:
[ moleculetype ]
; Name nrexcl
TRS      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OA     1  TRS      O1     1   -0.119  15.9994
     2         H     1  TRS     H13     1    0.032   1.0080
     3       CH2     1  TRS      C1     1    0.087  14.0270
     4      *CCL4  *   1  TRS       C     2    0.055  12.0110
     5       CH2     1  TRS      C3     2    0.049  14.0270
..

.newitp
[ moleculetype ]
; Name nrexcl
TRS      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OA     1  TRS      O1     1   -0.119  15.9994
     2         H     1  TRS     H13     1    0.032   1.0080
     3       CH2     1  TRS      C1     1    0.087  14.0270
     4      *CCl4 *    1  TRS       C     2    0.055  12.0110
     5       CH2     1  TRS      C3     2    0.049  14.0270
...
29 Mart 2011 16:41 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Then, what should I do?
>>
>>
> You've somehow created a topology that does not conform to the requirements
> of the force field.  Fix it so that it does.
>
> -Justin
>
>  29 Mart 2011 16:36 tarihinde Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> yazdı:
>>
>>
>>
>>
>>    ahmet yıldırım wrote:
>>
>>        Dear Justin,
>>
>>
>>        There is "CCl4  12.011   ;     carbon in carbontetrachloride
>>        (solvent)" in the gromos43a1.ff/atomtypes.atp file.
>>        But I still have the error "Atomtype CCL4 not found".
>>
>>
>>    Exactly as I said, capitalization is your issue.  CCl4 and CCL4 are
>>    not the same.
>>
>>    -Justin
>>
>>        2011/3/29 Justin A. Lemkul <jalemkul at vt.edu
>>        <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>>
>>        <mailto:jalemkul at vt.edu>>>
>>
>>
>>
>>
>>           ahmet yıldırım wrote:
>>
>>               Dear users,
>>
>>               Force field: 43a1
>>               water model: spc
>>
>>               After this command:grompp -f em.mdp -p topol.top -c
>>        solvated.gro
>>               -o em.tpr
>>
>>               I have the following error:
>>
>>               Fatal error:
>>               Atomtype CCL4 not found
>>
>>               What should I do?
>>
>>
>>           Use an appropriate atom type.  The issue is probably
>>        capitalization
>>           somewhere, i.e. CCl4 rather than CCL4.  See atomtypes.atp.
>>
>>           -Justin
>>
>>
>>               --         Ahmet YILDIRIM
>>
>>
>>           --     ========================================
>>
>>           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> <http://vt.edu> | (540)
>>
>>        231-9080
>>
>>           http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>           ========================================
>>           --     gmx-users mailing list    gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>
>>           <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>
>>
>>           http://lists.gromacs.org/mailman/listinfo/gmx-users
>>           Please search the archive at
>>           http://www.gromacs.org/Support/Mailing_Lists/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
>>        <mailto:gmx-users-request at gromacs.org>
>>           <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>.
>>
>>           Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>        --         Ahmet YILDIRIM
>>
>>
>>    --     ========================================
>>
>>    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    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    http://www.gromacs.org/Support/Mailing_Lists/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
>>    <mailto:gmx-users-request at gromacs.org>.
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>
> --
> ========================================
>
> 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    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110329/ee2c9f68/attachment.html>