> Hey all > > I'm trying to do a simple FEP within a simple protein, which seems to > make things simple...but as you may expect...it is anything else than > that. > > What I'm trying to do is morphing a Tyrosine into a Phenylalanine in > OPLSAA. > Therefore the CZ is changed from the type of TYR to the type of PHE. > The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a > dummy (PHE). So this is very simple. We checked the tpr-dump and > everything looks fine (except, maybe, we missed it). Now, in the > position-restraint run (where state B should not be regarded by the > system), the OH-proton moves on top of the OH-oxygen and the simulation > crashes after a while. We then performed a FEP from TYR to TYR (so A- > and B-state are the same) and the system runs.
The OH-proton seems to be constrained to the CZ of the aromatic ring, so it ocupies its proper position when moves on top of the OH-oxygen. It shoud be contrained to the "new" HZ. See Pearlman JMB (1995) 248, 696-717 > The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? > Gerrit and me think of a bug somewhere. > > Regards > > -- > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > ------------------------------ > > Message: 5 > Date: Tue, 7 Nov 2006 14:31:21 +0100 > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] invalid order of directive moleule type > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Harpreet, > > Regarding the message "invalid order ...", check the archives of this > mailing list. Further note that you shouldn't use the gmx (ffgmx) > force field, but should choose one of the Gromos force fields (united > atom), OPLS or Encad (all-atom). > > Specific to your problem is that there is a mismatch between the names > of atoms in the .pdb file and the names in the residue database (.rtp) > file of the force field you chose. Usually, it's best to modify the > names in the .pdb file to match those in the .rtp file. > > By the way, since you're new to Gromacs.., have you tried the > MD/Gromacs tutorial from the MD group in Groningen? If not, it may be > a good start to get to know gromacs. At present the Groningen group is > off the air, but I've mirrored the site at: > > http://nmr.chem.uu.nl/~tsjerk/MDCourse/ > > Hope it helps, > > Tsjerk > > On 11/7/06, merc mertens <[EMAIL PROTECTED]> wrote: > > if i were you, i would rather adapt my pdb file to an existing > forcefield as ffgmx, than trying to generate a new forcefield that fits > to your pdb with prodrug. the first option seems much easier to me. > what i mean is, if you change the names of you FAD atoms to the ones > you see in the *rtp they will be recognized by pdb2gmx. > > > > -------- Original-Nachricht -------- > > Datum: Tue, 07 Nov 2006 11:35:47 +0000 > > Von: "harpreet singh" <[EMAIL PROTECTED]> > > An: gmx-users@gromacs.org > > Betreff: [gmx-users] invalid order of directive moleule type > > > > > Hi All, > > > I am new to this package and want your help. I am trying to use > GROMACS to > > > study energy minimization and molecular dynamics for FAD molecule. > I am > > > having the following problems. > > > 1. I tried to run pdb2gmx for PDB file for FAD downloaded from > > > http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used > the > > > gromacs force field . The program gave the following error: - > > > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb > > > Opening library file > /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb > > > Opening library file > /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb > > > > > > Back Off! I just backed up fad_test.top to ./#fad_test.top.1# > > > Processing chain 1 (53 atoms, 1 residues) > > > There are 0 donors and 0 acceptors > > > There are 0 hydrogen bonds > > > ------------------------------------------------------- > > > Program pdb2gmx, VERSION 3.3.1 > > > Source code file: pdb2gmx.c, line: 393 > > > Fatal error: > > > Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms > > > while sorting atoms > > > On comparing topology file (ffgmx.rtp) for FAD entry i was surpried > to see > > > that it has atom type enteries OP1, OP2 instead of O1P, O2P in > downloaded > > > PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp > (for > > > FAD) and O3P was missing in this file. I am attaching the files > herewith. > > > > > > 2. I tried to make .top and .gro files (fad92.top and fad.gro > > > respectively) > > > ,using PRODRG2 server. and used them with grompp commad > > > > > > grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr > > > > > > This resulted in the following error. > > > > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# > > > checking input for internal consistency... > > > calling /usr/bin/cpp... > > > processing topology... > > > Cleaning up temporary file gromppfYcUxi > > > ------------------------------------------------------- > > > Program grompp, VERSION 3.3.1 > > > Source code file: topio.c, line: 388 > > > > > > Fatal error: > > > Invalid order for directive moleculetype, file ""fad92.top"", line > 15 > > > ------------------------------------------------------- > > > > > > "Oh, There Goes Gravity" (Eminem) > > > > > > Kindly guide me to solve this problem. > > > Thanks in advance > > > > > > Harpreet Singh > > > > > > _________________________________________________________________ > > > Use your PC to make calls at very low rates > > > https://voiceoam.pcs.v2s.live.com/partnerredirect.aspx > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > 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/mailing_lists/users.php > > > > -- > > Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! > > Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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/mailing_lists/users.php > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > post-doc > NMR, Utrecht University, > Padualaan 8, > 3584 CH Utrecht, the Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > > > ------------------------------ > > Message: 6 > Date: Tue, 07 Nov 2006 10:31:34 -0300 > From: "Mauricio Sica" <[EMAIL PROTECTED]> > Subject: [gmx-users] Re: Re: (dH/dl) calculation > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Tanks David > > Exactly: I`d want to calculate "dG/dl for some particular component of > the energy". Why? I did 2 FEPs, so I have two Delta_Gs for a mutations > in > 2 states: folded and unfolded. Both Delta_Gs are positive values. The > difference between them (Delta_Delta_G) is the value I was looking for. > This value agrees with experimental value of Delta_G of unfolding > between > 2 mutant proteins. Now, I want to know what is stabilizing or > destabilizing each state with respect the other. Analysis of each > component (e.g. Coul-SR:Prot-Prot) is impossible: it happens that Im > searching a delta_E of < 10 Kcal between a magnitude of 10E6. So I > thought that if I could obtain a <dE/dl> for a component and then > integrate them along lambda (TI method), I could get some idea about > its > magnitude. > > Mauricio > > > Mauricio, > > > > > That was exactly what I wanted to know. From one hand, because I > just > > > wanted to know it and, from the other hand, because I think that if > I > > have > > > some idea about how this calculus is carried out, I was able to > > estimate a > > > Delta_E for some energy components, for example, > > Coul-SR:Protein-Protein > > > by means of calculating the corresponding <dE/dl> (even when I know > > that > > > the value is not a state function as stated in the Mark & v > Gunsteren > > > paper). Maybe I should have started from this point. Is it posible? > > > > I'm sorry, I have no idea what you're asking here. Are you talking > > about trying to calculate a dG/dl for some particular component of > the > > energy? That doesn't sound useful, to me, since the components > > generally are all interdependent. And if you are trying to separate > > out the contribution of different components to the total dG/dl, this > > would require source code modifications, in general. Again, if you > can > > be more specific about what exactly you want to do (what problem are > > you trying to solve?) people may be able to be more helpful. > > > > David > > > > > > > > Message: 6 > > > > Date: Mon, 6 Nov 2006 10:19:05 -0800 > > > > > > > Mauricio, > > > > > > > > I'm somewhat confused by your question and notation. However, I > > think > > > > the basic answer is something like this: In molecular dynamics, > you > > > > know the Hamiltonian from which you are sampling; call it H(x,p, > > l), > > > > where x denotes all of the positions, p the momentums, and l > > lambda. > > > > This, of course, is closely linked to the potential energy. > Anyway, > > at > > > > any snapshot, you can simply take the derivative dH(x,p,l)/dl, > and > > you > > > > have dH/dl at that snapshot. This is usually straightforward > since > > you > > > > know the dependence of all of the terms in your Hamiltonian on > > lambda, > > > > so you actually have the functional form for dH/dl as well -- so > it > > > > just involves taking the appropriate combination of positions, > > > > momentums, etc. This is of course all handled internally by the > > code. > > > > <dH/dl>, then, is just the time-average of dH/dl, which can be > > > > evaluated every step by the code. > > > > > > > > I am not sure if that's helpful at all, as I'm not entirely sure > > what > > > > problem you're having. After all, whenever you do TI calculations > > in > > > > GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for > > every > > > > snapshot in an xvg output file. Are you just confused about how > the > > > > code gets this (I think I just answered that above), or are you > > trying > > > > to figure out how to use it? If you're confused about how to use > > it, > > > > try to ask a question that relates to the specific issue you're > > > > confused about. > > > > > > > > Best wishes, > > > > David Mobley > > > > UCSF > > > > > > > > > > > > On 11/5/06, Mauricio Sica <[EMAIL PROTECTED]> wrote: > > > > > Dear experts > > > > > > > > > > I am doing FEP (thermodynamic integration method) simulations. > > > > > I have a questions about <dH/dl> calculation in GROMACS. > > > > > Take in mind equation 3.77 from the GROMACS 3.3 manual. > > > > > There, dA/dl is calculated as > > > > > > > > > > dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = > <dA/dl>NVT;l > > } > > > > > > > > > > where SS are doble integrals (sorry for the notation). > > > > > > > > > > My question is: how is (dH/dl) (in the middel-term of the > > equation) > > > > > calculated? > > > > > My idea is that the difference V(L=1)-V(L=0) is calculated for > > every > > > > time > > > > > step (irrespective of the lambda value of the simulation) and > > <dG/dl> > > > > is > > > > > the time average of that difference. > > > > > > > > > > <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 > > > > > > > > > > > Is this correct? > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 31, Issue 23 > ***************************************** > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
