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

Hi Justin/Zhong Zheng, > > Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. > The problem is that, without -ignh, pdb2gmx expects all atoms (including H) > to be present in the .pdb file. If you are using a crystal structure, this > requirement will not be satisfied. >

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 for

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 computer

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

Zhong Zheng wrote: You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. Yes, you would have to rename all N-terminal ALA as NALA, as well as specify the correct Amber residue names for all other amino acids in your structure (i.e.,

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

Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N-terminal alanine would actually be calle

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

Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I ex

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

What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structu

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

hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in

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

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 of residue ALA in the file ff???.hdb (see the manual)". It's a warning message. I c