Justin, Could you provide me with the example of the server where I could obtain Gromac's itp topologies for the charmm ff? I know many such servers which could be useful only for preparation systems for NAMD program.
By the way recently I've made parametrization of my cGMP molecule by means of ATB server. In the below example you can see that the charge distribution is differs from the PRODRG example of that molecule which I've posted yesterday. Does that charge distribution more suitable for the 54a force field? [ atoms ] ; nr type resnr resid atom cgnr charge mass total_charge 1 NT 1 _N4H N2 1 -0.832 14.0067 2 H 1 _N4H H22 1 0.416 1.0080 3 H 1 _N4H H21 1 0.416 1.0080 ; 0.000 4 NR 1 _N4H N1 2 -0.715 14.0067 5 H 1 _N4H H1 2 0.427 1.0080 6 C 1 _N4H C2 2 0.775 12.0110 7 NR 1 _N4H N3 2 -0.691 14.0067 8 C 1 _N4H C4 2 0.431 12.0110 9 NR 1 _N4H N9 2 -0.227 14.0067 ; 0.000 10 C 1 _N4H C8 3 0.220 12.0110 11 HC 1 _N4H H01 3 0.162 1.0080 12 O 1 _N4H O6 3 -0.556 15.9994 13 C 1 _N4H C6 3 0.669 12.0110 14 C 1 _N4H C5 3 0.026 12.0110 15 NR 1 _N4H N7 3 -0.521 14.0067 ; 0.000 16 OE 1 _N4H O4* 4 -0.429 15.9994 17 CH1 1 _N4H C1* 4 0.429 13.0190 ; 0.000 18 CH1 1 _N4H C4* 5 0.000 13.0190 ; 0.000 19 OA 1 _N4H O5* 6 -0.422 15.9994 20 P 1 _N4H PAQ 6 0.971 30.9738 21 OM 1 _N4H OAR 6 -0.613 15.9994 22 OA 1 _N4H O3* 6 -0.382 15.9994 23 OA 1 _N4H OAS 6 -0.617 15.9994 24 H 1 _N4H H03 6 0.497 1.0080 25 CH2 1 _N4H C5* 6 0.319 14.0270 26 CH1 1 _N4H C3* 6 0.247 13.0190 ; -0.000 27 CH1 1 _N4H C2* 7 0.200 13.0190 28 OA 1 _N4H O2* 7 -0.614 15.9994 29 H 1 _N4H H8M 7 0.414 1.0080 ; 0.000 James 2012/12/5 Justin Lemkul <jalem...@vt.edu>: > > > On 12/5/12 1:39 PM, James Starlight wrote: >> >> Justin, >> >> Indeed the force field is the 54a7 ( modiffied version of the 54a6). >> >> The main reason of using GROMOS ff in that case was the topology of >> ligands which could be easily created by means of prodrg or ATB. On >> other hand I've never worked with the protein-ligand complexes in >> charmm ff for instance. >> > > Well, you get out what you put in. A recent paper > (dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed > very poorly for simulating nucleic acids. There are others, but that's just > a recent one. If you're choosing a force field because it makes life easy, > be prepared to defend your results if they are of poor quality or defend a > lot of wasted time while you re-do the simulations :) > > There are servers that produce CHARMM topologies and other programs that > will convert AMBER topologies into Gromacs format as well. I would suggest > you evaluate all the options available. > > >> By the way is there any suitable builing blocks (implemented in the >> rtp enties of the gromos ff) which could be used for charge >> assignment? >> > > That depends on the functional group. If it's also found in proteins, yes. > If not, then maybe but probably not. > > > -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 -- 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