Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? > > > On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> >> this atom is the CG atom of the phosphate I added to the protein. >> But how can I find out by what it is punished? >> > > Visualization. > >> This is the topology for this residue in the aminoacid.rtp file. I added >> it manually. The parameter are from the amber parameter database >> (http://www.pharmacy.manchester.ac.uk/bryce/amber/): >> >> [ TYP ] >> [ atoms ] >> N N -0.516300 1 >> CA CT 0.275503 2 >> HA H1 0.008223 3 >> CB CT -0.354052 4 >> HB1 HC 0.110326 5 >> HB2 HC 0.110326 6 >> CG CA 0.119728 7 >> CD1 CA -0.198938 8 >> HD1 HA 0.137143 9 >> CE1 CA -0.284884 10 >> HE1 HA 0.177179 11 >> CZ C 0.452616 12 >> OH OS -0.534452 13 >> H H 0.293600 14 >> CE2 CA -0.284884 15 >> HE2 HA 0.177179 16 >> CD2 CA -0.198938 17 >> HD2 HA 0.137143 18 >> C C 0.536600 19 >> O O -0.581900 20 >> P P 1.393213 21 >> OP1 OH -0.752821 22 >> OP2 O2 -0.822464 23 >> OP3 O2 -0.822464 24 >> H1P HO 0.423316 25 >> [ bonds ] >> N H >> N CA >> CA HA >> CA CB >> CA C >> CB HB1 >> CB HB2 >> CB CG >> CG CD1 >> CG CD2 >> CD1 HD1 >> CD1 CE1 >> CE1 HE1 >> CE1 CZ >> CZ OS >> CZ CE2 >> OS P >> CE2 HE2 >> CE2 CD2 >> CD2 HD2 >> C O >> -C N >> P OP1 >> P OP2 >> P OP3 >> OP1 H1P >> >> [ impropers ] >> -C CA N H >> CA +N C O >> CG CE2 CD2 HD2 >> CZ CD2 CE2 HE2 >> CD1 CZ CE1 HE1 >> CG CE1 CD1 HD1 >> CD1 CD2 CG CB >> CE1 CE2 CZ OH >> >> >> Additionally I had to add an entry in the ffbonded file in the part [ >> dihedraltypes ] >> >> CA CA C OS 4 180.00 4.60240 2 ; >> >> Here I am not completely sure about the entry because I could not find a >> source for this combination of atoms. >> But there is already an entry for the combination >> CA CA C OH >> Which has the same parameters. >> Could this be the problem? >> >> And if it could be, can you please give me hint where I can find >> parameters for it? Because I really could not find it. >> > > Potentially - if you haphazardly assign parameters, you may get unexpected > results. There is a cited reference for the TYP parameters at the website > above. I would suggest looking there first, and if there is nothing > listed, > then contact the corresponding author of the study that first used/derived > the > parameters. > > Additionally, if you freeze a part of the protein's structure, you prevent > any > existing clashes from being resolved. That may be the root of the issue. > > -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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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