Justin, Thanks again for explanation.
It's interesting that above parametrization made by ATB have cased the system to crash within first ps of modeling ;) (On the contrarythe system with the ligand made by prodrg have been very stable during 100ns). I ve tried to re-parametrized my molecule by another algorithm implemented in ATB ( am1 instead of pm3 which was used in the crashed simulation). James 2012/12/6, Justin Lemkul <jalem...@vt.edu>: > > > On 12/6/12 2:39 AM, James Starlight wrote: >> 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. >> > > Google "CHARMM ligand topology in Gromacs" (without the quotes) - the first > > result is what you're looking for. > >> >> 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? >> > > Given that PRODRG generally produces very bad charges, just about anything > is > better ;) > > Nucleotide parameters already exist in 54A7, I don't see why you necessarily > > have to create them from scratch. In general, these charges look pretty > good, > but note that DGUA already exists and can describe most of your molecule > already. The cyclic part is the only trick, but the nucleobase parameters > should be the same in cGMP and DGUA, given the nature of Gromos96 > parameterization. > > -Justin > >> [ 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 > > -- > ======================================== > > 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? 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