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

[Hua Li]

Dear all,   Would anybody tell me how to do it?  I don't understand clearly what's meaning of those parameters in pull.ppa with AFM otion?  Thanks a lot!
		Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.___
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] Constructing New Metal-Containing Topologies in OPLS

[M. Jake Pushie]

Hello gmx'ers,

I've been developing new residue topologies for the OPLS FF. These are
backbone-bound Cu-complexes, where the metal is coordinated directly to a
deprotonated amide N-atom, such as is observed at the N-terminal end of
serum albumin. I’m getting reasonable results, but unfortunately reviewers
seem to have had no end of complaints about the way we have represented
these things, so I'm hoping some experts out there could offer some useful
suggestions on how I might proceed with the modeling, or at least hint
that I really am on the right track.

Here's our current procedure:
1. Starting geometry for backbone atoms and the metal centre from X'tal
structure
2. Harmonic potentials for Cu-ligand bonds
3. Harmonic potential for the backbone atoms immediately around the metal
centre (these are planar complexes)
4. 1-4 pairs list updated to include the copper 1-4 interactions in the
models
5. CHELPG charges calculated using B3LYP/6-31G(d) from an optimized X'tal
geometry of the metal coordination site (at that same level of theory)

The main complaints of our models have been:
(1) the CHELPG charges that come out of the calculations are too small and
would favour hydrophobic-types of interactions. One reviewer seems to be
suggesting we start out with ion-like charges on the metal and ligands and
go from there. I don't really like this idea as it's not consistent with
the way the charges are derived for OPLS. Also any other charge-derivation
method would no longer be consistent with OPLS(!). Comparing the backbone
and side chain charges I calculate with their related atoms in similar
molecule fragments in the OPLS force field they differ by less than 5-10%
in most cases, except those directly involved in metal-coordination (which
is not unexpected).
(2) putting a harmonic potential on backbone dihedrals about the metal
centre makes these things too flat. I say: Since Cu binds into the
backbone, it replaces an H-atom and therefore the dihedral angle from Cu
across the backbone to the carbonyl O-atom is actually somewhere between
160-180 degrees, and without explicitly entering the local dihedral angles
based on X'tal data the force field only has the Cu-ligand bonds and
backbone angles holding it in place, but nothing else to define local
coordination geometry and backbone orientation.

Does anyone who has done CHELPG charge derivation have suggestions on the
CHELPG charge comments above? I'm using a radius of 1.4 A. for Cu2+. The
complexes are overall charge-neutral, and the CHELPG charge on Cu usually
comes out to be between 0.6 to 0.8 for all of the related complexes I've
calculated (I have data for more than 20 related species in various
protonation states and with different amino acids).  This apparently low
charge density (instead of something closer to 2+) at Cu may be because it
is bound by two formally anionic backbone amide N-atoms that are
deprotonated.

Also, I have recently run B3LYP/6-31G(d) geometry optimizations and
frequency calculations for a large number of hydrated Cu2+ complexes with
various ligands, and am using the force constants from the frequency
calculations (in mDyne/Angstrom, scaled by 60230) in the harmonic bond
potentials for the copper ligands. Does anyone know if it is reasonable to
expect an appreciable change in the magnitude of the force constant that
is calculated depending on the overall charge metal complexes (i.e. 1+,
2+, neutral, etc.)?

Jake Pushie

Ph.D. Candidate
Structural Biology Research Group
University of Calgary
Calgary, AB
CANADA



___
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] N-terminal and C-terminal modifications

[Mark Abraham]

List User wrote:

What is the best approach to handle N and C-terminal modifications
(e.g. formylation, chemical modification)?  Is it better to define
custom residue types or to adjust the termini database?  Thanks in
advance for your advice.


I would suggest custom residue types and/or termini, rather than 
modifying existing termini in the termini database and forgetting some 
time in the future that they are modified and wrongly re-using them for 
something else.


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] Fatal Error: moleculetype K is redefined

[Dallas B. Warren]

---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891

Fatal error:
moleculetype K is redefined
---

I believe this error is due to your forcefield files, the .itp files
that you have included.  You have some how doubled up.  May be trace
back through each .itp file that you have included.

Was just trying to do a search of the list to check to ensure that was
correct, but with the new website doesn't appear to be working correctly
yet.

Hope that helps some.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
___
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] Fatal Error: moleculetype K is redefined

[Venky]

Hi,While trying to setup a membrane inserted protein simulation I get this following error while running grompp command. % grompp -v -f em.mdp -c br1.pdb -p example.top -o br_emin.tpr
Generated 1369 of the 2211 non-bonded parameter combinationsExcluding 3 bonded neighbours for Protein_A 1
Cleaning up temporary file gromppjh3WI9---
Program grompp, VERSION 3.3.1Source code file: toppush.c, line: 891
Fatal error:moleculetype K is redefined
---But there are no moleculetypes K in my simulation and I have not generated any ions yet. I also had to do setup other lipids but again ended up in the same error. Please help...thanks in advance... below are the details of my input files.
EM.mdp optionstitle = BR_POPCcpp = /usr/bin/cpp ; the c pre-processordefine = -DFLEXIBLEconstraints = noneintegrator = cgdt = 0.002 ; ps !nsteps = 1000nstlist = 5ns_type = grid
rlist = 0.9coulombtype = PMErcoulomb = 0.9rvdw = 1.4fourierspacing = 0.12fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 4ewald_rtol = 1e-5optimize_fft = yes;; Energy minimizing stuff
;emtol = 1000.0emstep = 0.01TOP File input#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp"#include "
br.top" ;; protein topology#include "ions.itp"#ifdef FLEX_SPC#include "flexspc.itp"#else#include "spc.itp"#endif[ system ]; nameBR_POPC
[ molecules ]; name    numberProtein 1POPC    56SOL 4412--- -- Venky KrishnamaniGraduate Student, Dr. Janos K. Lanyi LabUniverisity of California, Irvine
Irvine, CA(949) 232-3021
___
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: request

[David van der Spoel]

sina wrote:
 
Dear developers,
I am a member of Computational Chemistry research group at university of 
Tehran. In one of our recent projects, we needed software for executing 
our MD calculations. In these respect, we chose GROMACS software because 
of its great utilities in MD simulations. We’ve gotten source codes and 
other related programs from www.gromacs.org and installed them 
successfully. we also executed the GROMACS demo example (gmxdemo) 
successfully, but, the version of software that was written in the 
output files was gromacs.3.1.4 in despite of the fact that we had 
installed the gromacs.3.3.1 version. Then, we tried to run the tutorial 
examples. Although, for one of them (speptide) the process was 
implemented successfully, but, for the other examples (water, methanol 
and mixed) surprisingly we got the following error when we tried to 
execute grompp –v command:
 
creating statusfile for 1 node...
 
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

WARNING 1 [file grompp.mdp, line unknown]:
Unknown left-hand init_step in parameter file
 
WARNING 2 [file grompp.mdp, line unknown]:

Unknown left-hand nbfgscorr in parameter file
 
WARNING 3 [file grompp.mdp, line unknown]:

Unknown left-hand nstcheckpoint in parameter file
 
WARNING 4 [file grompp.mdp, line unknown]:

Unknown left-hand table-extension in parameter file
 
WARNING 5 [file grompp.mdp, line unknown]:

Unknown left-hand gb_algorithm in parameter file
 
WARNING 6 [file grompp.mdp, line unknown]:

Unknown left-hand nstgbradii in parameter file
 
WARNING 7 [file grompp.mdp, line unknown]:

Unknown left-hand rgbradii in parameter file
 
WARNING 8 [file grompp.mdp, line unknown]:

Unknown left-hand gb_saltconc in parameter file
 
WARNING 9 [file grompp.mdp, line unknown]:

Unknown left-hand implicit_solvent in parameter file
 
WARNING 10 [file grompp.mdp, line unknown]:

Unknown left-hand andersen_seed in parameter file
 
Fatal error: Too many warnings, grompp terminated
 
The version of software that we saw in the output log file of the 
speptide example was gromacs.3.1.4 too. So we have two problems:
a) we have installed the 3.3.1 version but in the output log files we 
see 3.1.4.
b) we can’t run” water”, “methanol” and “mixed” tutorial examples 
because of the mentioned error and warnings that are appeared when we 
run grompp –v.
We searched the FAQ to solve the problem, but, we didn’t find any useful 
comment.. I appreciate all of your notification and instructions.
 
Best Regards;
Sina 
It seems that you have two version installed. You don't say which OS you 
use though, but please check the command

"which mdrun"
it will tell you which version you are using.

Plesea put further questions on the mailing list
 



Blab-away for as little as 1¢/min. Make PC-to-Phone Calls 
 
using Yahoo! Messenger with Voice.



--
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

[gmx-users] Details of force field

[arunima singh]

  
Hi,
Can somebody tell me where can i get the details about the G43a1 force field or can someone send me the paper by van Gunsteren 1996 on the same? 
Thanx,
Arunima






___
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