[gmx-users] error in converting charmm to gromacs !!

[Chanchal]

Hi All/Justin,
   I got the *.atp file from Mark Abraham and now it is not complaining
about ON2b atom type. But now I am getting the following error while I was
trying to create *.top file using the command:
/Users/parimalkar/gromacs-4.0.5/bin/pdb2gmx_d -ff charmm -f
step5_assembly.pdb -p topol.top -o dopc.pdb

Program pdb2gmx_d, VERSION 4.0.5
Source code file: ter_db.c, line: 87

Fatal error:
Reading Termini Database: expected 3 items of atom data in stead of 1 on
line
       N      NH3        14.0027    -0.3000
-------------------------------------------------------

Please help me !
Thanks
Chanchal


On Tue, Sep 29, 2009 at 11:42 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Chanchal wrote:
>
>> Hi All,
>>    I am have built a DOPC+water (tip3p) system in www.charmm-gui.org <
>> http://www.charmm-gui.org>. I converted *.itp file from CHARMM *.prm file
>> using Mark Abraham's script. I placed these *.itp files into the GMXLIB
>> directory. I have also edited FF.dat file and add a line "ffcharmm CHARMM
>> 27" and updated the line number. Now when I execute the command:
>>  /Users/parimalkar/gromacs-4.0.
>>
>> 5/bin/pdb2gmx_d -ff charmm -f step5_assembly.pdb -p topol.top, I got the
>> error message
>> "Fatal error:
>> Library file ffcharmm.atp not found in current dir nor in default
>> directories.
>>
>> (You can set the directories to search with the GMXLIB path variable)"
>>
>>
>>
>> Now when I copied the ffcharmm27.atp to ffcharmm.atp, and executed the
>> same command, then I got the error message:
>>
>>
>> Program pdb2gmx_d, VERSION 4.0.5
>> Source code file: resall.c, line: 138
>>
>> Fatal error:
>> Atom type ON2b (residue TP1) not found in atomtype database
>>
>> But I saw that ffcharmm.rtp (Yuguang Mu's file that I got from Mark
>> Abraham) contains ON2b. So how can I fix this error? Is it problem with
>> ffcharmm.atp? Should I not copy ffcharmm27.atp to ffcharmm.atp?
>>
>>
> The atomtype database is the .atp file, not the .rtp.  If the atom does not
> appear in the .atp file, you won't be able to use that type without defining
> parameters for it.
>
> -Justin
>
>  Thanks
>> Chanchal
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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