Re: [gmx-users] Smooth surface
On Tuesday 07 November 2006 08:46, David van der Spoel wrote: Tsjerk Wassenaar wrote: Hi Alex, I think you're best off describing the wall with particles. You can freeze them to a specific position (make it a freeze-group) and set all interactions between them to zero. You can tune your particles to be hydrophilic or hydrophobic. Hope it helps, If that really is not what you want, then please write down some equations how you would treat a hydrophilic wall. Just a Lennard Jones is not very complicated, and we have actually done something like that in the past (Wensink et al. Langmuir 16 (2000), p. 7392). I need Lennard-Jones interactions in Z direction between walls and Oxygens of water molecules. And second, repulsion function (also in Z direction) between atoms of peptides and walls. I think that it is possible to introduce periodic boundary conditions only in x and y directions? -- Alex Krukau Physical Chemistry II a University Dortmund tel: + 49 231 755 3938 fax: + 49 231 755 3937 ___ gmx-users mailing listgmx-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
Re: [gmx-users] Re: Molecular volume
...msms can calculate the surface of an atom list (generated from a pdb). This surface is triangulated and calculating the volume from a triangulated surface should be very easy. Regards Martin ___ gmx-users mailing listgmx-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
[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 listgmx-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
Re: [gmx-users] invalid order of directive moleule type
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 + 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 listgmx-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 listgmx-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
Re: [gmx-users] invalid order of directive moleule type
harpreet singh wrote: 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. You cannot expect pdb2gmx to do magic. It needs a rational way of identifying what molecule you are trying to use. In order to do that, it will match, first, residue name (from pdb) to building block (in rtp). Second, it will match atom names using some tricks to account for common variations in names, because one cannot assume a defined order of the atoms within a residue/molecule/building block. If pdb2gmx fails to match atom names, you will have to help it by (manuall) matching the atoms in your pdb file with those in the rtp. According to your taste, you can either rename atoms in the pdb (to match the rtp), or make a new building block in the rtp and rename atoms there (to match the pdb, but be aware that building block names in the rtp must be unique *and* match the residue name in the pdb). Fatal error: Invalid order for directive moleculetype, file fad92.top, line 15 You probably didn't include the ffgmx.itp in your .top file (first, atomtypes, bondtypes etc. must be defined before you can define a moleculetype). Read the manual, please, especially those beautiful chapters on forcefields and on topologies! -- Groetjes, Anton _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ gmx-users mailing listgmx-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
[gmx-users] Strange problem with simple FEP (bug?)
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 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/ ___ gmx-users mailing listgmx-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
Re: [gmx-users] invalid order of directive moleule type
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 + 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 listgmx-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 listgmx-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 ___ gmx-users mailing listgmx-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
[gmx-users] Re: Re: (dH/dl) calculation
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/dlNVT;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
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Re: [gmx-users] Strange problem with simple FEP (bug?)
Update: Checked it with the Amber99 port. Same strange habit. It occured with another protein (system), too. 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/ Maik Goette wrote: 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 whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards ___ gmx-users mailing listgmx-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
[gmx-users] Re: gmx-users Digest, Vol 31, Issue 23
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 + 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
[gmx-users] GROMACS Speed
Hi,i use GROMACS i like it because it is so fast. But, i would like to know if GROMACS "cut corners" ? Otherwise, why is it is so fast?if you have a fortran compiler on an Opteron box, GROMACS does not use the assembly loops. Right? So, why is it blazingly fast?o. Sponsored Link Try Netflix today! With plans starting at only $5.99 a month what are you waiting for?___ gmx-users mailing listgmx-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
Re: [gmx-users] GROMACS Speed
Omololu Akin-Ojo wrote: Hi, i use GROMACS i like it because it is so fast. But, i would like to know if GROMACS cut corners ? Otherwise, why is it is so fast? if you have a fortran compiler on an Opteron box, GROMACS does not use the assembly loops. Right? So, why is it blazingly fast? o. gromacs does not cut corners... Most important we do not compute stuff that we know will give zero as a result anyway, this gives 20-30% compared to other codes. Single precision is a factor of two faster than double, assembly is a factor of two faster than C/Fortran, and finally our innerloops are completely unrolled, this probably also gives a factor of 1.5. So if you multiply it all you have a significant factor (even in double precision). Sponsored Link Try Netflix today! With plans starting at only $5.99 a month what are you waiting for? http://clk.atdmt.com/NFX/go/yhxxxnfx002913nfx/direct/01/ ___ gmx-users mailing listgmx-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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
Re: [gmx-users] Strange problem with simple FEP (bug?)
Maik Goette wrote: Update: Checked it with the Amber99 port. Same strange habit. It occured with another protein (system), too. please submit a bugzilla. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
Re: [gmx-users] Re: Re: (dH/dl) calculation
Mauricio, 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 I'm 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. OK, I have two comments about this, and then I'll give you an alternative suggestion, which is somewhat better, but probably still not great. First, the comments: (1) To obtain component-wise dG/dl values, you would need to modify the source code (probably fairly extensively) to get GROMACS to save components of the dG/dl, not just the total. You are of course free to do this, but I can't help. (2) This would probably not be particularly informative, as you'll probably find that most of the difference is in Lennard-Jones and Coulomb interactions -- in the unfolded state, between the protein and the solvent, and in the folded state, between the protein and itself (and possibly also solvent). Maybe you learn something from that, but I doubt you'll learn anything terribly surprising, given the amount of work it will take (from (1)). Something you could do that would be somewhat less work than the above, and probably about as informative, is to break the transformation into several parts, where you (for example) first change the charges involved in your mutation, and then change the Lennard-Jones interactions. Then you'll get several component free energies -- a free energy of changing the electrostatics, and a free energy of changing the LJ interactions. These are, of course, path-dependent, but still, comparing the charging component, for example, between the unfolded and folded states may give you some idea of whether the difference is largely electrostatic or not. Otherwise, you may want to look at structural order parameters to figure out what is going on -- i.e. the radial distribution function of water around the residue of interest, number of hydrogen bonds, things like that. One other comment on the approach of looking at components of the potential energy: Keep in mind, the force field was parameterized to get the total potential energy right (as a function of the coordinates), *not* to give correct individual components. Personally (although others may disagree) if I were reviewing a paper that tried to make a significant case by looking at the breakdown of a free energy by components in the way you are describing, I would want to see some validation on a simple system where the right answer is known in order to show that this approach really works. In other words, I wouldn't trust that the results are right just because you can do it. Best wishes, David 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
Re: [gmx-users] Strange problem with simple FEP (bug?)
Maik, 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. I am not an OPLS guy myself, and I don't know the details of your transformation, so I'll just tell you one possibility, and you'll have to decide whether it could apply in your situation. Sometimes, if you are disappearing a Lennard-Jones site that still has some amount of electrostatics, it can begin to interpenetrate with other atoms which either do not have Lennard-Jones interactions (hydrogens in some force fields) or which do (depending on the combination rule you use). Obviously, this is bad because (for example) protons can move on top of oxygens and cause blowing up. A classic example of this is, for example, if I am turning off the LJ on an oxygen site at the same time as turning off the charges on that oxygen. In many FF's, water hydrogens lack LJ interactions, so they can come and overlap with the oxygen I'm disappearing, which is still charged (at least to some degree) and cause a fusion type event. I don't know if that's what's going on for you, but you might think about it -- do you have any atoms that you're disappearing, and are there other atoms which the combination rules would allow to overlap with those? The way I get around this problem in my calculations is to always turn off electrostatics on any atom I'm disappearing prior to modifying the LJ parameters, so that I never have a charged atom which is being treated using the soft-core potentials that allow overlap. Not sure if that's your problem -- just a thought. David 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/ ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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
Re: [gmx-users] GROMACS Speed
Thanks, David. i appreciate your response.o.David van der Spoel [EMAIL PROTECTED] wrote: Omololu Akin-Ojo wrote: Hi, i use GROMACS i like it because it is so fast. But, i would like to know if GROMACS "cut corners" ? Otherwise, why is it is so fast? if you have a fortran compiler on an Opteron box, GROMACS does not use the assembly loops. Right? So, why is it blazingly fast? o.gromacs does not cut corners...Most important we do not compute stuff that we know will give zero as a result anyway, this gives 20-30% compared to other codes.Single precision is a factor of two faster than double, assembly is a factor of two faster than C/Fortran, and finally our innerloops are completely unrolled, this probably also gives a factor of 1.5.So if you multiply it all you have a significant factor (even in double precision). Sponsored Link Try Netflix today! With plans starting at only $5.99 a month what are you waiting for? ___ gmx-users mailing listgmx-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-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Check out the all-new Yahoo! Mail - Fire up a more powerful email and get things done faster.___ gmx-users mailing listgmx-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
[gmx-users] g_rdf
Hi GMX ers, I posted this question earlier, but did not receive a reply. Hope to get an answer this time around.I was wondering what could be the origin of a spike at close distances when I compute the RDF of N-P atoms in a lipid bilayer system (0.25 nm) I tried using -cut option and also increasing the nrexcl to 5 in the N and P atoms ( to avoid intramolecular contributions?) And yet, I still get that spike. Any insight would be very helpful Thanks Rama Everyone is raving about the all-new Yahoo! Mail.___ gmx-users mailing listgmx-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
Re: [gmx-users] g_rdf
Rama Gullapalli wrote: Hi GMX ers, I posted this question earlier, but did not receive a reply. Hope to get an answer this time around. I was wondering what could be the origin of a spike at close distances when I compute the RDF of N-P atoms in a lipid bilayer system (0.25 nm) I tried using -cut option and also increasing the nrexcl to 5 in the N and P atoms ( to avoid intramolecular contributions?) And yet, I still get that spike. maybe your index file is incorrect, or the trajectory does not match the tpr (did you use shuffling?) Any insight would be very helpful Thanks Rama Everyone is raving about the all-new Yahoo! Mail. http://us.rd.yahoo.com/evt=42297/*http://advision.webevents.yahoo.com/mailbeta ___ gmx-users mailing listgmx-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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
Re: [gmx-users] temperature shooting up
Cherry Y. Yates wrote: Dear Mark, Thanks for your help, I followed you instruction, and I can get stable temperature after I remove the temperature coupling. In this case I used the flexible spc itp file. However if I use a rigid spc.itp, after remveing the temperature coupling, the system temperature is shooting up from 300K to thousands degree, the total energy is going up also instead of fluctuating. I attached both the itp files and grompp.mdp files. Let me know what could be wrong. It is really wired to me. The change in the model physics from flexible to rigid is severe one - almost all of the water molecules won't fit the rigid geometry, and will thus be in a high-potential-energy state. If the constraint-enforcing algorithm conserves energy, then that potential energy has to be converted to kinetic energy. Then if the simulation lacks temperature coupling, it is at constant energy and the temperature will be necessarily high. Actually you say you observe rising energy - this is probably because your timestep is too large to conserve energy at this very high temperature (and thus atomic velocity). So the take-home lesson is not to do two perturbations of your model physics at one time. If you really want to start with a flexible water model with temperature regulation and end up with rigid water model at without temperature regulation, do the water transition with temperature coupling still on to give the energy somewhere to flow - to the external bath. I expect you'd need a short temperature coupling constant to make this work in practice. Once that's stable, *now* try taking off temperature coupling. This suggests the question, why you'd want to do this flexible-rigid transition in an equilibration? It would be simpler to start in the rigid domain, and to do energy minimization to correct any geometries before starting MD simulations. Mark ___ gmx-users mailing listgmx-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
Re: [gmx-users] Using a different potential function
David, Thanks for your reply. These are bonded interactions, but there are some angle-angle cross terms involving products of cosines of angles. I could probably try to convert them to one of the available bonded functions. Daniel ___ gmx-users mailing listgmx-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
