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 >| 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 <[EMAIL PROTECTED]> 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<<
em.mdp
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tip3p.itp
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ions.itp
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