But the rest of the command was correct? Since I only want to minimize the phosphates which I added to the protein I want to use the freeze option to make sure that the other residues will not change. But how can I say gromacs that it shell make an exception and do not freeze the phosphate of the residues where I added the phosphate?
Thank you!! > > > On 9/4/12 11:21 AM, [email protected] wrote: >> Hi everybody, >> when I want the program "pdb2gmx" only to create a topology file but not >> to change anything at the protein. Not even adding hydrogen atoms to the >> protein. >> Because my protein already has hydrogen atoms. I only added one residue >> and I want to minimize this residue now. >> >> >> Do I have to call it like this: >> >> pdb2gmx -f inputProtein.pdb -o outputProtein.gro -p protein.top -i >> posre.itp -water none -ff amber03 -ignh >> >> Is that right? >> > > No. The use of -ignh tells pdb2gmx to ignore any input hydrogens and > build its > own. That is the exact opposite of what you are trying to do. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
