Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

One of my issues is now solved. As you guessed, the PBD was in an improper format. After solving this small issues, I read about the need for an lipids.itp and pope.itp file. I found these tutorial (link below) for the itp file construction. Can I adept these steps for the construction of corre

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

Leonhard Henkes wrote: Thanks for your reply, my whole pdb file includes an equilibrated membrane bilayer, constructed with VMD for NAMD. I used the CHARMM27 FF while constructing it. Now, I wanted to convert this system for a run in Gromacs. To solve my issus, I divided my system into four

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

Thanks for your reply, my whole pdb file includes an equilibrated membrane bilayer, constructed with VMD for NAMD. I used the CHARMM27 FF while constructing it. Now, I wanted to convert this system for a run in Gromacs. To solve my issus, I divided my system into four new pdb's (ion, water, lipi

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

kalav...@gmx.net wrote: Dear gromacs users, I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and "Long Bond" warnings.

[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

Dear gromacs users, I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and "Long Bond" warnings. In other threads, the lipid