[gmx-users] Re: ffamber and ions

[Alan]

So, as requested:

for ions.spc I got info from http://www.somewhereville.com/?p=114

In attach files you may need to reproduce what I am doing here. Assuming you
have ffamber installed and GMX 3.3.
Copy ions.itp and tip3p.itp to your _gromacs_/top/ folder.

tip3p.itp was modified by me.

I use Mac OSX 10.4.11 intel with Fink

My commands based on 1BVG.pdb (you can get it at www.pdb.org):


grep 'ATOM  ' 1BVG.pdb>| Protein.pdb


sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\
\ \ 1/g \

| sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \

| sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \

| sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g >|
ProteinAmber.pdb


pdb2gmx -ff amber99 -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top
-water tip3p


editconf -bt triclinic -f Protein2.pdb -o Protein2.pdb -d 1.0


genbox -cp Protein2.pdb -cs ffamber_tip3p.gro -o Protein_b4ion.pdb -p
Protein.top


grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr


echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -nname Cl -nn 4
-norandom


sed s/7274/7270/ Protein.top > temp; echo "Cl  4" >> temp; \mv temp
Protein.top


grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr # total
charge: 8.000000e+00 !!!!


mdrun -v -deffnm em


Many thanks for your attention.
Cheers,
Alan

-------------------
Can you show us your modified ions.itp file (just the Cl part) and the exact
command options you used for genion?
Thanks,
Vignesh

On Thu, Jul 3, 2008 at 7:44 AM, Alan <alanwilter at gmail.com> wrote:

> Hi List,
> To people using ffamber.
>
> I have ffamber with ions.itp modified to recognise ffamber ions. All seems
> fine and working.
>
> So, I have a protein, net charge +4 e. In the pdb file there no ions and no
> water. I modify the pdb as said in ffamber instructions. All fine.
> Then, I add water and hence I use genion to neutralise my system. I add 4
> Cl. All fine.
>
> However when using grompp for preparing the inputs for a minimisation, I
> got a warning saying that my system is now +8 e. It happens no matter what
> ion I use with ffamber (being it pos or neg, or value 2). It's like if
> genion were counting only the ions and not reading the ion's charge value.
>
> I know it's reading my modified ions.itp file because otherwise genion will
> fail to process.
>
> Has someone else seen that? Any comments?
>
> Despite this, I can minimise and carry on MD on my system. Is there any
> other to definitely know if GMX is computing the right charge values?
>
> Many thanks in advance.
> Cheers,
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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