[gmx-users] Unable to add ions...
sharada at ccmb.res.in
Tue Oct 10 09:52:21 CEST 2006
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....
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-
> 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
>> 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
>> 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
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