[gmx-users] topology treatment in free energy calculations - possible bug

entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophy

[gmx-users] topology treatment in free energy calculations - possible bug_2nd

afterwards, even if the values are crap for the B-state... 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 E

Re: [gmx-users] topology treatment in free energy calculations -possible bug

Berk Thanks for the clarification. I was aware of A-values copied to B-values, when no B-values in the FF exist, but actually this was new to me. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassber

Re: [gmx-users] energy perturbation

erent free energy calculation methods and how they are used in GROMACS. Especially have a look into "softcore" and be aware of using it JUST for vdw morphing... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational bioph

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Hi Try the -ff option of pdb2gmx, if you're not able to get it working. This less complicated. pdb2gmx -f pdb.pdb -ff ffG43a1 Should work Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg

Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Chris This is, what I usually do, too. Still you need the parameters for your ligand from 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

Re: [gmx-users] Dihedral with parameters set to zero

No Holland-Speek here! ;) Anyway, you maybe right...:) 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

Re: [gmx-users] FEP trajectory errors

really know, if the A-parameters in the posre-file will be copied to B, too. Test that with a gmxdump. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 2

Re: [gmx-users] free energy calculation

methods, their pros and cons in general. Using a tutorial is not the only thing to do, to compute meaningful free energies. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Ger

Re: [gmx-users] How to remove H atom from residue in gro file?

lated residues according to these parameters: N Homeyer, AHC Horn, H Lanig, H Sticht - Journal of Molecular Modeling, 2006 This is for sure some work and you need an understanding of how GROMACS makes use of residue parameters and stuff, but its IMHO the best way to produce reasonable results. regar

Re: [gmx-users] a problem,Thank you

This has been discussed several times... Search the mailing list archive. 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 E

Re: [gmx-users] source code change

Avinash > Afterwards will I need to compile it again? Don't want to be mean, but are you sure, after such a question, you can actually write and understand C-code? Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics d

Re: [gmx-users] FEP trajectory errors

hould also mention, that, especially with such large perturbations as a full DNA-base, you should split your topology into 2, where you switch off the QQ hardcore and the VdW softcore in two steps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical &

Re: [gmx-users] source code change

You're welcome... 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[a

Re: [gmx-users] FEP trajectory errors

Do really all atoms "freeze". So also the atoms, which are not perturbed? Can you post your mdp-file? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel.

Re: [gmx-users] Virtual site and constraints

rge there and no mass. Thats, how virtual sites work. If you want to use a "free energy dummy", you may have to use a different approach. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11

Re: [gmx-users] Rugged dG/dlambda when turning off charges

The point is: You want to do a severe perturbation. May I inform you, that I tried morphing base pairs for 3 years and now quitted? ;) Anyway, if you have such a strong perturbation, you should think about a different setup, like softcore for vdw and harcore for qq. Regards Maik Goette, Dipl

Re: [gmx-users] Rugged dG/dlambda when turning off charges

steps could help you in getting a better total error and stuff. Again, from my experience I can tell you, that calculating free energies from letting nucleotides appear/disappear is really no fun. If you come up with a solution yourself, I would be highly interested in it. Regards Maik Goette, Dipl.

Re: [gmx-users] RE : FEP : separating components of dgdl

I think, there are some "best" parameters :) Ich tested them with some smaller systems and found, that sigma=0.3 and alpha=0.25 seem to perform quite well. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics

Re: [gmx-users] Rugged dG/dlambda when turning off charges

f the base, which leads to a very heavy perturbation and therefore a very "spiked" dG/dl. 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 F

Re: [gmx-users] MD of DNA-protein complex AND non-protein inhibitor

es in the best case against some experimental data. Good luck 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 : mgoet

[gmx-users] Deviations in free energies with slow growth (single and 3-step process)

ll hardcore... Any ideas? 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

Re: [gmx-users] FEP : separating components of dgdl

dihedral from the forcefield and write them in the topology. BTW, in your case its not problematic anyway, cause they are the same :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goetti

Re: [gmx-users] RE : FEP : separating components of dgdl

> Maik, what is the power you are using for soft core ? As Berk and others suggested, sc-power = 1. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49

Re: [gmx-users] pdb2gmx: Adding non standard residues and molecular moieties

Sorry, with this question, probably no one can help you. You're probably missing a FF entry. Which FF are you actually using? Search the mailing list/Wiki for how to parametrize a molecule! Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & comp

Re: [gmx-users] Deviations in free energies with slow growth (single and 3-step process)

tty" results. Do you think, 7 kJ/mol lies within the usual error of free energy calculations? If, one could never resolve reliably smaller free energy differences and the whole method won't be applicable for say drug screening or so. Regards Maik Goette, Dipl. Biol. Max Planck Insti

Re: [gmx-users] (no subject)

but if you use exactly the files given there (and add sc-power = 1), you should get values, which are close to the experimental one (I guess, cause a tutorial won't make sense, if the files don't yield the desired value). Sorry, but more help is hard to give with so few information. R

Re: [gmx-users] toluene tutorial sc-power value

#x27;t know the error. How to post the numbers: Exp. value (+error) and your calculated value (+error) ? From those I could tell you if something is terribly wrong or not. :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational bioph

[gmx-users] Strange dgdl-value together with lincs

pike in the first step extremely strange. Additionally it only occurs, when using shake or lincs as constraint solver. I guess, in a longer process it will contribute to the integral in a neglectable manner, but maybe theres some bug. The latest CVS shows the same behaviour. Any comments on that?

Re: [gmx-users] Strange dgdl-value together with lincs

0.0 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 :

Re: [gmx-users] (no subject)

grompp cant find your mdp-file. Please give a subject next time, as well as more detailed information. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551

Re: [gmx-users] toluene tutorial sc-power value

ause the only effect is a change of the sign to +19 and therefore worse. Can you show me the topology, you made? As far as the free energy experts here discussed it, sc-power=2 shouldn't be the lambda-dependance of choice. I can agree to that from my simulations. regards Maik Goette, Di

Re: [gmx-users] toluene tutorial sc-power value

topology seems not too bad. I'm not used to that forcefield, though. As a general suggestion, its always better to sample many lambda points and each longer, than wasting time with using sc-power=2 :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theore

Re: [gmx-users] toluene tutorial sc-power value

Fine :) So forget what I wrote before...I mentioned exactly that :) 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 E

Re: [gmx-users] Strange dgdl-value together with lincs

ntuitively, I'd say it shouldn't differ in the free energy of both. Thanks again for the help 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 F

Re: [gmx-users] Strange dgdl-value together with lincs

n that case). I will sample the system a bit longer (66ns for each case in total) and make a gz-download. Anyway, to me they look normal. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettin

Re: [gmx-users] Strange dgdl-value together with lincs

I used, was without the november bug fix, so I can't tell which fix helped with the problem. Sorry for that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel.

Re: [gmx-users] problem with undistribution of water

That "problem" is called periodic boundaries. Try inserting a second bilayer to get, at least on one axis, a water layer between the two lipid layers, if you want to prevent PBC for a part of the waters. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry T

Re: [gmx-users] Ki estimation

You can't compare a Ki directly from the MD AFAIK. What you could do is, computing the free energy difference between two ligands and compare it to the difference in Ki (which actually is closely related to the famous Kd), if that helps you Regards Maik Goette, Dipl. Biol. Max P

Re: [gmx-users] traj.trr

Read the manual... 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]gwd

Re: [gmx-users] Black whole simluations

Thank you Sir If this was fake or not...Me and my dear colleagues had a good laugh, anyway...also about the nice comments. Maybe this inspires: http://www.youtube.com/watch?v=qiSkyEyBczU "Black hole sun, won't you come" Regards Maik Goette, Dipl. Biol. Max Planck Institute

Re: [gmx-users] set up topology in free energy calculations

at charge difference is possible. However, I think this would lead to a very bad equilibrated system and no reasonable results. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen

Re: [gmx-users] GTP in topology

It means: Include the topology, you got from the PRODRG server as an itp file in your general topology file If you don't know, what I mean, read the manual about including topologies... Btw, more info, more answer regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophy

Re: [gmx-users] free energy calculation

So, obviously, no one knows how to do that by g_lie. Most people here compute free energies by TI. Do some background reading and find out yourself how it works. Posting mails twice or more won't help you regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chem

Re: [gmx-users] Re: combining differently-generated force-fields

Hi This IS a textbook-chapter. It seems very fresh. Just found it here on Bert's desk. After a very rough inspection, I don't expect anything new or any breakthrough, though. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical &

Re: [gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example.

nergy. Therefore, I think, you have to switch the sign of your calculations and you're fine. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 231

Re: [gmx-users] Free energy of discharging and then recharging not zero

tions. This doesn't sound promising, I know, but actually, I fear, there is no proper solution. Maybe you should morph G to A or T to C or something like that, where just a few atoms have to be perturbed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry T

Re: [gmx-users] Free energy of discharging and then recharging not zero

idine morph (or vice versa), I'm still convinced, that you would have to sample for ages to get a converged system, though. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goetting

Re: [gmx-users] Strange dV/dl profile in free energy calculation

Hi Always hard to tell, cause one doesn't know, if your parameters are correct ;) Anyway, the LJ-part always looks a bit unintuitive, probably due to softcore. I saw similar curves in my base-deletions. I think, you can trust the curve. Regards Maik Goette, Dipl. Biol. Max P

Re: [gmx-users] Zinc (Zn) parameters

the charge on your ZN in its environment via QM and see, if it remains, where it should. I observed, that ZN likes to leave its place, when complexed to 2 CYS and 2 HIS, given a charge of ~ 0.7. Maybe, also dependent on your interest, QM/MM could help here. Regards Maik Goette, Dipl. B

Re: [gmx-users] soft-core potential in combination with PME (sorry, again)

ou with the basic code for that. 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

Re: [gmx-users] Problems using grompp and amber force field

er? If not, one proton in your first base may be the wrong type...but this shouldn't result into your error. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel.

Re: [gmx-users] Residue 'SIA' not found in residue topology database

or try Antechamber (?) from the AMBER-package. After calculating reasonable partial charges, you can try to get the LJ-Parameters and other stuff from existing FF-entries. How to build the FF-entries, i.e. mainly an RTP-entry, one can obtain from the manual. Happy LEGOing Regards Maik Goette, Dipl

Re: [gmx-users] FEP with real or dummy charges?

ore atoms. If you want to have the charge sitting on a special atom, just change that charge explicitly, although I'm really not sure, if that's the way, one should go. Hope you get some help from that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysi

Re: [gmx-users] antechamber installation

Just wanted to mention that ;) 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 mgoe

Re: [gmx-users] atom type not found error

Hard to tell from that amount of information... Seems, you don't include a forcefield... Please describe in more detail, what you exactly did and maybe post the head of your topology-file... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theore

Re: [gmx-users] FEP with real or dummy charges?

No. I said, you may want to perturb all partial charges in the site, where the netto +1 charge sits OR place a virtual site somewhere in between, to grow a point charge, whereas I'm not sure, if a point charge is, what you want. Regards Maik Goette, Dipl. Biol. Max Planck Institut

Re: [gmx-users] Problems with forcefield amber99 in Gromacs

aiting for the Do-whatever-I-mean-tool... 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]

Re: [gmx-users] Total energy with different energy groups

Random velocities? 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 mgoette

Re: [gmx-users] Question about DNA simulation

Because it is? The masses are defined in the .atp file. I dont't know how GROMACS handles the stuff, but that is sufficiantMaybe Eric was a bit lazy... Why do you care for that...? Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & comp

Re: [gmx-users] Question about DNA simulation

add a new atom type to the nb-section? Just out of curiosity... 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 E

Re: [gmx-users] Question about DNA simulation

Hi I never had to change masses in the nb.itp and I ran lots of simulations with the amber-Port...Are you sure, that you had no dummies with mass zero or so? REgards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics departmen

Re: [gmx-users] free energy calculation and constraint distance?

WHAM (if I remember correctly) Now, it's up to you, which method you favormay also depend on your system/question Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen German

Re: [gmx-users] free energy perturbations and B-parameter specifications

Hi You have to be more specific... Did you just do one sim for Gly->Ala? Are you sure, you did the simulations in a way, you can compare it to exp. results? (think about doing the perturbation once in water and once in vacuum or so) Regards Maik Goette, Dipl. Biol. Max Planck Institute

Re: [gmx-users] Mutagenesis

he best one can doand, btw., expect to invest some time to get this working. Hope, this helps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 55

Re: [gmx-users] dummy atom definition prob in FEP

s (eps and sigma=0) and no charge, but still the original mass. 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 Emai

Re: [gmx-users] Constrains and TI

ree energy difference by using different distance restraints, anyway. Regards P.S. As I just saw it. Inform yourself about the difference between CONSTRAINTS and RESTRAINTS (there is an important one...) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & co

Re: [gmx-users] dummy atom definition prob in FEP

ation... 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

Re: [gmx-users] Constrains and TI

building the famous costly random number generator... 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

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

As Mark suggested. If you have the parameters for your ATP, build an RTP-entry and afterwards, give the protein together with ATP into pdb2gmx... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 3

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Be aware, that you can't use the ouput with every forcefield... Attaching the gro-file to your protein gro at the proper position (right after the protein) and building the correct topology should do the job. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theore

Re: [gmx-users] Re: question about free energy. Gromacs user

you have to apply simply more distance restraints along the whole ligand. Maybe you should stick to methods like TI or pulling, which are implemented and heavily used within GROMACS... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computati

Re: [gmx-users] Pull code methods?

to compare your sim with, IF you want to compare :) Hope that helps 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 E

Re: [gmx-users] Residue 'UNK' not found in residue topology database

important rule to obey before posting to this mailinglist: RTFM... bye 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

Re: [gmx-users] Pull code methods?

an once... Maybe you should intensively search the archive for such things... 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

Re: [gmx-users] proper force fields for fullerene

Have a look at the manual and search the mailing list. You want to simulate a not recognized/parameterized molecule. Therefore you have to implement the parameters. How thats done can be found e.g. in the wiki. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry

Re: [gmx-users] Help! A dummy atom definition problem!

call it H instead... 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 mgo

Re: [gmx-users] Re: "Impulsive" motion resulting from AFM pulling

. Is the position you plot the com or the pull group? 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 : mgoett

Re: [gmx-users] ffamber updates

port, but maybe it's better if you do, because you have more experience in building the amber-ports. What do you think? I didn't read the paper according to your 99sb-port yet. Do you think it makes sense to switch from the amber99 to amber99sb? Regards Maik Goette, Dipl. Biol. Max

Re: [gmx-users] gromacs result

free energy of bindingexcept you are very luckyIF you are that lucky, play lottery instead and enjoy life ;) In fact it's (citating Mark) another expensive random number generator... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theore

[gmx-users] Minor Bug in latest stable release update

gards -- 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

Re: [gmx-users] How to specify .mdp file for position restrained simulation?

he manual) The probability of getting good results and no crap increases dramatically with following the two points above... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germa

Re: [gmx-users] free energy calculations in charged systems

h) or Berk have some more sound comments on that. 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 : mgoett

Re: [gmx-users] ATP, GTP and REX

Hi You can use the AMBER ports for 3.3.2, I'd say. 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 : mgoet

Re: [gmx-users] afm pulling

t via mail. 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.d

Re: [gmx-users] problem with ffamber94bon.itp

Berk, you're right. That's the way it goes... I think, Eric Sorin mentioned that on his page, though. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel.

Re: [gmx-users] How to set constant pulling force in pull.ppa with AFM option?

you can derive the force-profile. 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.mp

[gmx-users] FEP softcore problematics

ns at lambda=0 & 1. Any suggestions? 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]m

Re: [gmx-users] FEP softcore problematics

that paper, but unfortunately didn't. It would be great, if you could give me some more info about it, cause I would like to have a look into it, at least. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fass

Re: [gmx-users] FEP softcore problematics

Thank you Berk and David I'll try the ways you suggested. 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 2

Re: [gmx-users] Problem simulating DNA

that (done by Eric Sorin). Then, you have to modify your PDB according to the FF. 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

Re: [gmx-users] Re: FEP softcore problematics

Welcome to the world of science... But I thought exactly the same as you do and therefore give a +1 to your mail...:) Regards (BTW: Sorry, for this needless spam...) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics departmen

Re: [gmx-users] free energy and fatal error

... More details, like your mdp-file, would be helpful. 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

Re: [gmx-users] free energy and fatal error

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 :

[gmx-users] OPLS entries Thiophosphate

and stuff from the xplor files)? 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

Re: [gmx-users] problem simulating DNA

imply isn't defined in the bon.itp. 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]

[gmx-users] Possible Bug GROMACS 3.3.1 - NMA

e's a bug. Any suggestions? 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

Re: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA

Yes, I'm using Cut-off. And the Error is reproducable. I'll post the bug report. 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 Fa

[gmx-users] Strange problem with simple FEP (bug?)

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. Regard

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