Re: [gmx-users] grompp error in peptide-membrane simulations

afsaneh maleki wrote: Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: >Fetal error : Atomtype LC3 not found! (this is

[gmx-users] grompp error in peptide-membrane simulations

Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: >Fetal error : Atomtype LC3 not found! (this is atomtype of the lipide) This i

Re: [gmx-users] grompp error in peptide-membrane simulations

Hi Tsjerk: thanks again for the full description of what i should to do. I did it and grompp runs ! cheers Maite On 3/3/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Maite, Indeed you shouldn't really run the lipids through pdb2gmx, but try to obtain a .itp file for a lipid, match

Re: [gmx-users] grompp error in peptide-membrane simulations

Hi Maite, Indeed you shouldn't really run the lipids through pdb2gmx, but try to obtain a .itp file for a lipid, matching the force field you're trying to use. What you can do is take one lipid and run it through pdb2gmx, using your favourite force field. Make sure that the resulting structure fi

Re: [gmx-users] grompp error in peptide-membrane simulations

maite lopez wrote: i've changed the atoms of the dppc.itp file by the atoms of the DPPC molecule that appear in the ffG53a5.rtp file (for example LC3 by CH3) and run grompp , but it gives : Fatal error: Atomtype 'C1' not found! I don´t know how to convert my lipids to ffG53a5. Could you ex

Re: [gmx-users] grompp error in peptide-membrane simulations

Thanks Tsjerk In the begining i tried to create the dppc.gro executing pdb2gmx ( pdb2gmx_331 -f dppc.pdb -dppc.gro -p dppc.top -i dppc.itp -ffG53a5 -water spc -ignh) i 've gived a lot of warnings. Warning: Long Bond (34-36 = 4.17214 nm) Warning: Long Bond (36-37 = 4.13444 nm) Warning: Long Bond

Re: [gmx-users] grompp error in peptide-membrane simulations

Hi Maite, grompp-error... helpful subject :) You're trying to combine ffG53a5 and ffgmx. Very bad idea (and not readily possible anyway, since atom type definitions and other things are incompatible). You have to convert your lipids to ffG53a5. Don't try to do it the other way around and convert

[gmx-users] grompp error in peptide-membrane simulations

Hi: This is the other part of my last email. I've done many things as suggested in mailing list for example: 1)If i don't include the lipid.itp file atomtype LC3 not found or if i put ";" in the line 9 of lipid.itp atomtype LC3 not found or if i put ";" in the line 9 of lipid.itp