Hi, Add the LA to the atoms block in the ff*nb.itp, using zero for all parameters. Check out for instance how the MW sites of water are listed. LA 0 0.0 0.000 A 0.0 0.0
Gerrit > > Date: Fri, 22 Jan 2010 23:22:30 +0900 > From: "yoochan,myung" <my...@kangwon.ac.kr> > Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works. > To: gmx-users@gromacs.org > Message-ID: <40b2aeda-8f01-4d91-ae44-2886f2401...@kangwon.ac.kr> > Content-Type: text/plain; charset=us-ascii > > Hi. > > I'm on QM/MM simulation (gromacs-gaussian03). > > I exactly followed under reference, but I could't success. > http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmvacuum.html#top > > > > I checked presence of two LA atoms in [ atoms] of TOP file. > > Also, I checked under [ dummies 2] and [ constraints ]in Top file. > (I think, [ dummies 2] = [ virtual_sites 2] but, [ virtual_sites 2] in 4.x.x > Gromacs, [ dummies 2] in 3.x.x) > > [ dummies 2] > 1279 906 904 1 0.72 > 1280 938 936 1 0.72 > > [ constraints ] > 906 904 2 0.153 > 938 936 2 0.153 > > > And then, I did GROMPP, I got this error message. > (In reference, there is a "run.scr " step which is multiple GROMPP and MDRUN > running scripts.) > > 'Atom type "LA" not found' > > > I think grompp doesn't recognize atom "LA" on [ atoms ] as dummies. > > Any suggestions? > > > Regards. > > yoochan, > > ------------------------------ > > Message: 2 > Date: Fri, 22 Jan 2010 13:02:50 -0500 > From: nishap.pa...@utoronto.ca > Subject: [gmx-users] cut-off > To: gmx-users@gromacs.org > Message-ID: <20100122130250.y57ap287284oo...@webmail.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hello, > > I wanted to know, if say my box is 30A (cubic) and if I set my > cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, > the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm > (to get half the box cut-off)? I am a little confused about that. > > Thanks. > > Nisha Patel > > > > > ------------------------------ > > Message: 3 > Date: Fri, 22 Jan 2010 13:10:29 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] cut-off > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4b59ea15.50...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > nishap.pa...@utoronto.ca wrote: >> Hello, >> >> I wanted to know, if say my box is 30A (cubic) and if I set my >> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, >> the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm >> (to get half the box cut-off)? I am a little confused about that. >> > > Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm are > zero. > It has no effect on, for example, Coulombic interactions. > > Most force fields have defined cutoffs that should be used in order to be > consistent with the original derivation of the parameter set, so it is > generally > inadvisable to make ad hoc changes to the cutoffs in order to meet some > arbitrary criterion. The minimum image convention specifies that your > longest > cutoff must always be less than half the smallest box vector. If you set up > a > system with a cutoff equal to exactly one half of a box vector, if that box > vector decreases even slightly (i.e., under the influence of pressure > coupling), > then you will be calculating spurious forces. > > -Justin > >> Thanks. >> >> Nisha Patel >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Fri, 22 Jan 2010 13:20:06 -0500 > From: nishap.pa...@utoronto.ca > Subject: Re: [gmx-users] cut-off > To: gmx-users@gromacs.org > Message-ID: <20100122132006.3azbohlydcw4c...@webmail.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > I see what you mean, so say if I am doing RDF, the values beyond 9A > would be bogus? > > > Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > >> >> >> nishap.pa...@utoronto.ca wrote: >>> Hello, >>> >>> I wanted to know, if say my box is 30A (cubic) and if I set my >>> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that >>> mean, the simulation will cut-0ff at 9A? Should I be changing that >>> to 1.5nm (to get half the box cut-off)? I am a little confused >>> about that. >>> >> >> Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm >> are zero. It has no effect on, for example, Coulombic interactions. >> >> Most force fields have defined cutoffs that should be used in order to >> be consistent with the original derivation of the parameter set, so it >> is generally inadvisable to make ad hoc changes to the cutoffs in order >> to meet some arbitrary criterion. The minimum image convention >> specifies that your longest cutoff must always be less than half the >> smallest box vector. If you set up a system with a cutoff equal to >> exactly one half of a box vector, if that box vector decreases even >> slightly (i.e., under the influence of pressure coupling), then you >> will be calculating spurious forces. >> >> -Justin >> >>> Thanks. >>> >>> Nisha Patel >>> >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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/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/mailing_lists/users.php > > > > Nisha Patel > MSc Candidate > Leslie Dan Faculty of Pharmacy > Department of Pharmaceutical Sciences > 144 College Street > Room 1172 > Toronto, ON > M5S 3M2 > Canada > Telephone: 416-978-1536 > > > > ------------------------------ > > Message: 5 > Date: Fri, 22 Jan 2010 13:32:55 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] cut-off > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4b59ef57.9010...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > nishap.pa...@utoronto.ca wrote: >> I see what you mean, so say if I am doing RDF, the values beyond 9A >> would be bogus? >> > > To a large extent, probably, but I don't think that I can say that absolutely > without context. For example, you've only shown us rvdw, what about > rcoulomb? > If it is longer for some reason, then this value will also influence the RDF. > Long-range electrostatics (i.e., PME) may have some effect as well, but I > don't > really have much detailed experience in doing that sort of thing. > > There is a nice section in the manual about RDF calculation, as well as an > example RDF plot for SPC water that should give you an idea of what to > expect, > in general. > > -Justin > >> >> Quoting "Justin A. Lemkul" <jalem...@vt.edu>: >> >>> >>> >>> nishap.pa...@utoronto.ca wrote: >>>> Hello, >>>> >>>> I wanted to know, if say my box is 30A (cubic) and if I set my >>>> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that >>>> mean, the simulation will cut-0ff at 9A? Should I be changing that >>>> to 1.5nm (to get half the box cut-off)? I am a little confused about >>>> that. >>>> >>> >>> Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm >>> are zero. It has no effect on, for example, Coulombic interactions. >>> >>> Most force fields have defined cutoffs that should be used in order to >>> be consistent with the original derivation of the parameter set, so it >>> is generally inadvisable to make ad hoc changes to the cutoffs in order >>> to meet some arbitrary criterion. The minimum image convention >>> specifies that your longest cutoff must always be less than half the >>> smallest box vector. If you set up a system with a cutoff equal to >>> exactly one half of a box vector, if that box vector decreases even >>> slightly (i.e., under the influence of pressure coupling), then you >>> will be calculating spurious forces. >>> >>> -Justin >>> >>>> Thanks. >>>> >>>> Nisha Patel >>>> >>>> >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> 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/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/mailing_lists/users.php >> >> >> >> Nisha Patel >> MSc Candidate >> Leslie Dan Faculty of Pharmacy >> Department of Pharmaceutical Sciences >> 144 College Street >> Room 1172 >> Toronto, ON >> M5S 3M2 >> Canada >> Telephone: 416-978-1536 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Sat, 23 Jan 2010 03:11:32 +0700 > From: akram gorji <lotus6...@gmail.com> > Subject: [gmx-users] question > To: gmx-users@gromacs.org > Message-ID: > <891238761001221211n5ecbbf80r51780dd475699...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or > rigid?which is better?thanks > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100123/ccb00433/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Fri, 22 Jan 2010 21:25:36 +0100 > From: David van der Spoel <sp...@xray.bmc.uu.se> > Subject: Re: [gmx-users] question > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4b5a09c0.2070...@xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/22/10 9:11 PM, akram gorji wrote: >> Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or >> rigid?which is better?thanks >> > Do you mean nano tubes? > > Try some literature search. Quite a bit has been done on this topic, > also with GROMACS. > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > ------------------------------ > > Message: 8 > Date: Fri, 22 Jan 2010 14:28:27 -0700 > From: Jose Tusell <jrta1...@gmail.com> > Subject: [gmx-users] diketopiperazine > To: gmx-users@gromacs.org > Message-ID: > <d0c164c71001221328q2151c25cn7615012f91304...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I'm trying to construct diketopiperazine with gromacs. The problem that I > have right now is forming the bond that unites the C and N termi to make the > cyclic peptide. I tried using specbond.dat but so far I've been > unsucessful. Here is my specbond.dat file and pdb file: > > specbond.dat > 8 > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 > CYS SG 1 HEME FE 2 0.25 CYS2 HEME > CYS SG 1 HEME CAB 1 0.18 CYS2 HEME > CYS SG 1 HEME CAC 1 0.18 CYS2 HEME > HIS NE2 1 HEME FE 1 0.2 HIS1 HEME > MET SD 1 HEME FE 1 0.24 MET HEME > CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 > TRP N 1 HISH C 1 0.2 TRP HISH > > whdikp.pdb > REMARK S 14 x 14 mn oif > ATOM 1 N TRP 1 -0.813 0.594 1.164 > ATOM 2 H TRP 1 -0.249 1.064 1.843 > ATOM 3 CA TRP 1 -0.264 -0.210 0.004 > ATOM 4 HA TRP 1 0.855 -0.244 0.066 > ATOM 5 CB TRP 1 -0.633 0.484 -1.321 > ATOM 6 HB1 TRP 1 -1.672 0.344 -1.531 > ATOM 7 HB2 TRP 1 -0.408 1.528 -1.262 > ATOM 8 CG TRP 1 0.205 -0.166 -2.397 > ATOM 9 CD1 TRP 1 0.227 -1.464 -2.727 > ATOM 10 HD1 TRP 1 -0.407 -2.173 -2.195 > ATOM 11 CD2 TRP 1 1.119 0.455 -3.258 > ATOM 12 NE1 TRP 1 1.166 -1.607 -3.796 > ATOM 13 HE1 TRP 1 1.401 -2.473 -4.259 > ATOM 14 CE2 TRP 1 1.673 -0.432 -4.078 > ATOM 15 CE3 TRP 1 1.485 1.803 -3.344 > ATOM 16 HE3 TRP 1 1.065 2.575 -2.699 > ATOM 17 CZ2 TRP 1 2.626 -0.117 -5.054 > ATOM 18 HZ2 TRP 1 3.035 -0.902 -5.690 > ATOM 19 CZ3 TRP 1 2.444 2.145 -4.320 > ATOM 20 HZ3 TRP 1 2.741 3.190 -4.402 > ATOM 21 CH2 TRP 1 2.990 1.222 -5.140 > ATOM 22 HH2 TRP 1 3.727 1.540 -5.878 > ATOM 23 C TRP 1 -0.816 -1.621 0.004 > ATOM 24 O TRP 1 -0.072 -2.712 0.004 > ATOM 25 N HISH 2 -2.331 -1.621 0.004 > ATOM 26 H HISH 2 -2.895 -2.093 -0.674 > ATOM 27 CA HISH 2 -2.881 -0.816 1.162 > ATOM 28 HA HISH 2 -4.000 -0.781 1.098 > ATOM 29 CB HISH 2 -2.516 -1.510 2.488 > ATOM 30 HB1 HISH 2 -1.564 -1.990 2.400 > ATOM 31 HB2 HISH 2 -2.494 -0.794 3.283 > ATOM 32 CG HISH 2 -3.591 -2.538 2.747 > ATOM 33 ND1 HISH 2 -3.867 -3.560 1.846 > ATOM 34 HD1 HISH 2 -3.399 -3.715 0.964 > ATOM 35 CD2 HISH 2 -4.447 -2.700 3.792 > ATOM 36 HD2 HISH 2 -4.608 -2.157 4.723 > ATOM 37 CE1 HISH 2 -4.846 -4.291 2.344 > ATOM 38 HE1 HISH 2 -5.219 -5.152 1.791 > ATOM 39 NE2 HISH 2 -5.203 -3.793 3.502 > ATOM 40 HE2 HISH 2 -5.932 -4.166 4.093 > ATOM 41 C HISH 2 -2.329 0.595 1.164 > ATOM 42 O HISH 2 -3.089 1.710 1.164 > > Thanks for any suggestions, > > Jose Tusell > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100122/a6297950/attachment.html > > ------------------------------ > > -- > 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/search before posting! > > End of gmx-users Digest, Vol 69, Issue 110 > ****************************************** -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- 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/search before posting! 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