[gmx-users] Unable to add ions...

[sharada]

Dear Dr. Tsjerk Wassenaar,

Thanks for replying . The force field I am using is ffG43a1.itp in 
Gromacs 3.1.4  version and I tried all combinations CL,CL- Cl - cl etc....
sharada


Tsjerk Wassenaar wrote:

> Hi Sharada,
>
> The name depends on the force field used (you didn't mention). You may
> need to try CL or CL-
>
> Best,
>
> Tsjerk
>
> On 10/10/06, sharada <sharada at ccmb.res.in> wrote:
>
>>
>>  Hello friends,
>>
>>  I am trying to simulate a protein of 36 residues (HBD1) in water . 
>> Since my
>> protein has net charge  of
>>  +4  I had to neutralize it by adding 4 chlorine ions using ' 
>> genion'. After
>> that I edited the .top file to add the required
>>  "ions.itp" and also reduced  the number of SOL molecules by 4 in the [
>> molecules ] line and added one line for  Cl     4
>>  to complete the top file. After this when I run the grompp program 
>> with the
>> new pdb file containing the ions. However it is not able to recognize 
>> the Cl
>> ions ...
>>  The following are the sequence of commands I give:
>>
>>  pdb2gmx -f HBD1pr.pdb -o HBD1prn.pdb -p HBD1pr.top -ignh
>>  editconf -f HBD1prn.pdb -o HBD1pr_box.gro -c -d 0.6
>>  genbox -cp HBD1pr_box.gro -cs spc216.gro -o HBD1pr_b4em.gro -p 
>> HBD1pr.top
>>  grompp -f em.mdp -c HBD1pr_b4em.gro -p HBD1pr.top -o HBD1pr_em.tpr
>>  genion -s HBD1pr_em.tpr -o HBD1pr_ion.pdb -nname Cl -nn 4 -nq -1 
>> -random
>>  I edit the HBDpr.top for including the "ions.itp" and modify the 
>> number of
>> SOL molecules
>>  and also add a line for Cl  ions. then delete the HBD1pr_em.tpr file to
>> create a new tpr file.
>>  rm HBD1pr_em.tpr
>>  grompp -f em.mdp -c HBD1pr_ion.pdb -p HBD1pr.top -o HBD1pr_em.tpr
>>
>>  the error is :
>>
>>  Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41#
>>  Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
>>  checking input for internal consistency...
>>  calling /lib/cpp...
>>  processing topology...
>>  Generated 135 of the 1081 non-bonded parameter combinations
>>  Excluding 3 bonded neighbours for Protein_B           1
>>  Excluding 2 bonded neighbours for SOL              1366
>>  Cleaning up temporary file grompp013645
>>  Fatal error: No such moleculetype Cl
>>
>>  Where am I  going wrong  I am not able to figure out.  Has anybody come
>> across such problem...please help with suggesions
>>
>>  sharada
>>
>>
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>
>