[gmx-users] protein falls apart in energy minimization

hi all I am running Gromacs on a protein consisted of three chains. But no matter how I tried, the protein always falls into three parts (corresponding to each chain) after a simple 2000 steps energy minimization. Can anyone help me please? Thanks. Zhong Zheng

[gmx-users] Questions about energy groups!

. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE new wiki: http://134.74.90.158/ ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] atom H is missing in the first residue in a chain

-missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c- terminus? How can I fix this? Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City

Re: [gmx-users] atom H is missing in the first residue in a chain

in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database

Re: [gmx-users] atom H is missing in the first residue in a chain

You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote: Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my

[gmx-users] How to treat an isolated iron (Fe 2+)

ligands and one Glu ligand. The total charge for the complex should be +1. Is there a good way to treat this isolated iron? Thanks a lot. Zhong Zheng ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] atom H is missing in the first residue in a chain

Thanks Justin. I fixed it this time. I basically renamed the terminal residues. The reason it didn't work last time is probably because some format problem. Thanks again. On Jan 14, 2009, at 2:50 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: You mean rename ALA as NALA in the .pdb