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 Planck

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

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 Goettingen Germany Tel

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

. 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 Theoretical

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 computational

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

. 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 2310 Fax : ++49

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 Biophysical

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

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 Germany Tel. : ++49 551 201

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 for Biophysical

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]gwdg.de

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 Planck

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 Theoretical

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

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. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email

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

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 Goettingen Germany Tel. : ++49 551

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

, 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 Fax : ++49 551 201 2302

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 : http

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. : ++49 551 201

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

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, Dipl. Biol. Max

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

). The 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 Theoretical

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 Email : mgoette

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

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 biophysics department Am

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

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? Regards -- Maik Goette, Dipl. Biol. Max Planck

Re: [gmx-users] (no subject)

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. Regards Maik Goette, Dipl

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

, 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 Institute for Biophysical Chemistry

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. : ++49 551 201 2310

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 computational

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

for that 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 Goettingen Germany

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

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 : mgoette[at]mpi

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

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 mgoette2[at]gwdg.de WWW

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 department Am

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

, 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 Fax : ++49 551 201 2302 Email

Re: [gmx-users] Virtual site and constraints

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 37077 Goettingen

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

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. Biol

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 Email

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[at]gwdg.de WWW

Re: [gmx-users] FEP trajectory errors

, 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. : ++49 551 201 2310 Fax : ++49 551

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 Germany

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]mpi

Re: [gmx-users] energy perturbation

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 biophysics department Am Fassberg

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 11 37077

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 Fassberg 11

[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 biophysics

[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 Email : mgoette

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

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 : mgoette[at]mpi-bpc.mpg.de

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

) 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 Germany Tel. : ++49 551

Re: [gmx-users] ffamber updates

, 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 Planck Institute for Biophysical Chemistry

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 Theoretical

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 : mgoette[at]mpi

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

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 mgoette2[at]gwdg.de

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] Pull code methods?

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 2302 Email : mgoette

Re: [gmx-users] Pull code methods?

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 Email : mgoette

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

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 : mgoette[at]mpi-bpc.mpg.de

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 computational

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]mpi

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 11 37077

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 37077

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

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. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de

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

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 Email : mgoette[at]mpi

Re: [gmx-users] Constrains and TI

, 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 computational biophysics department Am Fassberg 11 37077 Goettingen

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

... 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

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

(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 Germany Tel. : ++49

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 department Am

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 Email

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

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]mpi-bpc.mpg.de

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 mgoette2

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 Theoretical

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

. 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 Biophysical Chemistry Theoretical

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 mgoette2

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

? 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. : ++49 551 201 2310

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] soft-core potential in combination with PME (sorry, again)

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 mgoette2[at]gwdg.de

Re: [gmx-users] oplsaa with tip4p

Probably you have to rename MW to HW3 in your pdb-file...it's a known issue, I guess. Best 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

[gmx-users] Thiophosphate LJ-Parameters

. Best 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

Re: [gmx-users] Which force-field for DNA-protein complex ?

I'm using amber99 port most of the time. 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] Nucleic Acids -- Protonate ?

thought exactly the same...and btw...Mark, the one with the car mechanic was great...;) Best 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

Re: [gmx-users] free energy calculation

and then interpolates between them in a linear fashion (dependent of if you use soft-core or not). From this arises a yes for the second part of your question. If I'm wrong with that, I'm sure, someone who knows better will correct me quite fast. ;) Regards Maik Goette, Dipl. Biol. Max Planck Institute

Re: [gmx-users] about afm !

://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 . Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical

Re: [gmx-users] GROMACS AMBER DNA TERMINUS

for guanines, e.g. 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

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

in general resembles. Best 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] Partial charge distribution for metal ligating atoms

of all complex partners, the system should again be at charge 0. I can't see the problems, sorry. 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

Re: [gmx-users] protonated cys -S

Try renaming the Cys in the the PDB to CYS2. 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

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

Thanks, but that's indeed not the problem. I'm just doing a PR-run in state A. State B is not of interest in that case. Somehow GROMACS mixes things up internally, I guess. The bugzilla-entry has been placed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry

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

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

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

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 Fax : ++49 551

[gmx-users] OPLS entries Thiophosphate

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 mgoette2

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]mpi

Re: [gmx-users] Problem simulating DNA

for 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 : ++49 551 201

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 department Am

[gmx-users] FEP softcore problematics

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]mpi-bpc.mpg.de

Re: [gmx-users] FEP softcore problematics

, 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 Fassberg 11 37077 Goettingen

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 2302 Email : mgoette

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.mpg.de

Re: [gmx-users] afm pulling

. 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

Re: [gmx-users] First release, translation supporting PDB-(AMBER, GROMACS)

in GROMACS and IMHO makes sense. 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] First release, translation supporting PDB-(AMBER, GROMACS)

Thanx ! Hopefully, this can be implemented in the next GROMACS version. 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

Re: [gmx-users] How to make drug for OPLSA ff compatiable

You simply can't do that, right now. OPLS isn't implemented into PRODRG, yet (correct me, if I'm wrong). Therefore the atom-naming, etc. maybe wrong. Anyway...a more detailed documentation of the error would be very helpful. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical

Re: [gmx-users] nucleic acis simulation

Take the Amber-Port: http://folding.stanford.edu/ffamber/ http://www.gromacs.org/topologies/uploaded_force_fields/ffamber_v1.0-doc.tar.gz But beware of renaming atoms and residues before use. If you don't pdb2gmx will inform you about problems. Regards Maik Goette, Dipl. Biol. Max Planck

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