[gmx-users] ffamber and ions

Alan alanwilter at gmail.com
Thu Jul 3 12:03:30 CEST 2008

Sorry, sending again in plain txt
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 >|

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

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

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<<
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