[gmx-users] Error with polymer surface modeling

Dear users, I'm working on simulating protein interactions with polymer surface for tissue engineering applications. I have developed a primitive model of polymer surface of polystyrene using "genconf". I have obtained .gro and .itp files using prodrg. But now I face error when I use grompp thou

Re: [gmx-users] mdrun producing 0 steps, 0 ps

Hi Travis, It looks like grompp doesn't parse your .mdp file properly. You should get an mdout.mdp which contains the parameters as they ended up in your .tpr file. Check these against your .mdp file. Alternatively you can 'gmxdump' your .tpr file to check the parameters. Was the .mdp file origina

Re: [gmx-users] Missing H's in NADH topology?

Hi Rui, In the previous version of the gromos force field, the hydrogens on these groups would be collapsed to the carbons. In the newer force fields (53*) they are treated explicitly, but I think NADH has not yet been reparameterized. Cheers, Tsjerk On Mon, Jun 30, 2008 at 9:14 PM, Joaquim Rui

Re: [gmx-users] yet another question about PBC...

Hi, use trjconv Well, that's just to start the mail with it in stead of ending. g_rms (g_gyrate, g_rmsf, g_covar) are rather dumb programs, taking a structure, fitting it to a reference orientation and doing some stuff on it. They don't check for jumps over the PBC. PBC and fitting don't go too w

[gmx-users] force field

Dear all gmx users and developers, I am running a simulation of esters. However,i failed to allocate the force field of 1 of the Carbons. (I am using OPLS-AA force field) -C-C=C-C-C=C-C- * The Carbon atom labeled with symbol * cannot be identified. I checked the ffoplsaa.atp file but I

[gmx-users] mdrun producing 0 steps, 0 ps

Hello, I'm trying to perform an energy minimization on a Tubulin-GTP-GDP complex in a water solvent with sodium ions. I use the following command to setup up the minimization, > grompp -f em.mdp -c tubulin_b4em.gro -p tubulin3.top -o tubulin_em.tpr My energy minimization file em*.mdp is: tit

Re: [gmx-users] How to calculate dihedral angle ??

Chih-Ying Lin wrote: HI g_chi is designed to help user to calculate the dihedral angles. I have an organic compound and as the manual describes that .gro , .trr and ssdump.dat are the required input files to compute and collect the dihedral angles with time. g_chi is for use with the

AW: [gmx-users] How to calculate dihedral angle ??

You can use vmd for dihedral angle vs time plots. Download *.gro and *.xtc files and use label option in vmd for dihedral angles.   serdar --- Chih-Ying Lin <[EMAIL PROTECTED]> schrieb am Mo, 30.6.2008: Von: Chih-Ying Lin <[EMAIL PROTECTED]> Betreff: [gmx-users] How to calculate dihedral angle

[gmx-users] Missing H's in NADH topology?

Dear all, In the .rtp files for the gromos96 forcefield (G43a1, G43a2, G43b1, G45a3, G53a5 and G53a6), the aromatic hydrogens that should be bonded to the adenine and nicotinamide moieties are missing in NADH. Why is that so? Shouldn't these hydrogens be explicit? On the other hand, if I gener

Re: [gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??

This is a link to a table for the OPLS parameters showing the 0.35 for the Hydrogens in the RNH2  group (not RCH2NH2--my mistake). It is Table 2 on page 64. Again, my question is why Gromacs  uses 0.36 for the hydrogens in the non n-terminus NH2 group of the uncharged lysine molecule when the pu

[gmx-users] How to calculate dihedral angle ??

HI g_chi is designed to help user to calculate the dihedral angles. I have an organic compound and as the manual describes that .gro , .trr and ssdump.dat are the required input files to compute and collect the dihedral angles with time. For my case, .gro and .trr files are ready. How to prepar

Re: [gmx-users] Re: warning mesgs

is that fine if i change the SOL number in the top file created at the first step ? On Mon, Jun 30, 2008 at 1:50 PM, rams rams <[EMAIL PROTECTED]> wrote: > Here's where your problem is. This step is unnecessary! Once you have the > topology, there is no need to re-process with pdb2gmx. Once

Re: [gmx-users] Re: warning mesgs

Hi, I mistyped the command as you mentioned. I did used the following: grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p insu_pwi.top -o MM_insu.tpr Now the error is the following: turning all bonds into constraints... NOTE: System has non-zero total charge: -2.00e+00 processing coordinat

Re: [gmx-users] Re: warning mesgs

rams rams wrote: Dear Justin, I am absolutely sorry for the discomfort. Since this is the first time I am using Gromacs, so things are not clear to me so I am trying things very randomly thats why I could not keep update the things. Here I restarted every thing and have a look at and let me

Re: [gmx-users] Re: warning mesgs

Hi! I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems to me that you forgot to create the required insu_pwi2MM.gro file. In your last pdb2gmx command you just created insu_pwi2MM.pdb, and then the last grompp command cannot found the insu_pwi2MM.gro file. I think you ha

Re: [gmx-users] Re: warning mesgs

Dear Justin, I am absolutely sorry for the discomfort. Since this is the first time I am using Gromacs, so things are not clear to me so I am trying things very randomly thats why I could not keep update the things. Here I restarted every thing and have a look at and let me know your suggestions:

Re: [gmx-users] Segmentation fault with gromacs 3.3.3

Once again, in reply to myself I could state that gromacs-3.3.3 won't build correctly on debian systems with gcc-4.3 neither. gmxtest simple dumps the following information. *** glibc detected *** mdrun: realloc(): invalid next size: 0x082a20d0 *** === Backtrace: = /lib/i686/cmov/libc.

Re: [gmx-users] yet another question about PBC...

Ramon Crehuet wrote: Hi, Please don't flame me for asking yet another question about the "out of the box" and PBC issue. I've tried to RTFM, RTFML, but could not find the question I'm asking. I (think) I understand what PBC implies and the fact that "out of the box" makes no sense because the s

[gmx-users] yet another question about PBC...

Hi, Please don't flame me for asking yet another question about the "out of the box" and PBC issue. I've tried to RTFM, RTFML, but could not find the question I'm asking. I (think) I understand what PBC implies and the fact that "out of the box" makes no sense because the system is periodic and gro

[gmx-users] typo on manual 3.3 pdf

On gmx_manual-3.3.pdf, page 101, where one reads: However if you wat to specify N ... Should be, I guess: However if you want to specify N y Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cam

[gmx-users] FFGMX. Units of a constant.

Hi, What is the units for dihedral reastaints used in FFGMX? What confused me: /usr/share/gromacs/top/ffgmxbon.itp: CO2 0.000 167.360 C OM2 0.000 167.360 C NT2 0.000 167.360 x2top -h: -kb real 40 Bonded force constant (kJ/mo

Re: [gmx-users] Which ensemble for membrane proteins?

sudheer babu wrote: Hi everybody, I have read one review article( dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf ) about membrane proteins tells about POPC alone sim

[gmx-users] g_mindist possible bug - missing a frame

Dear Gromacs users, I used g_mindist in order to generate minimum distance between a certain protein and a ligand. I invoked -od (to generate xvg) and -o (to generate atom-pairs list). Following that, I aligned the atom-pairs columns next to the distance columns so to have a list of [protein

[gmx-users] Which ensemble for membrane proteins?

Hi everybody, I have read one review article( dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf ) about membrane proteins tells about POPC alone simulations should run in NPT but not in NVT conditions. Regarding protein run in both some time NPT remain time

Re: [gmx-users] Re: warning mesgs

It would be helpful if all of this was on one thread, with replies embedded. I have sent several replies to your questions, all of which have gone unacknowledged. It makes it very difficult for anyone (myself or someone else) to give advice if we don't know what you're doing or what you've tr

[gmx-users] Re: gmx-users Digest, Vol 50, Issue 97

Try installing development version: openmotif-devel Hi I want to use grace 5.1.9 (normally xmvgr). each time i do installation using " ./configure", it prompts motif not found . So i tried to find free softare openmotif (it can do the same work as motif). Having successfully installed openmo

Re: [gmx-users] step size too small

Minnale, Please do read the following: http://wiki.gromacs.org/index.php/Errors This one's in there. Tsjerk On Mon, Jun 30, 2008 at 11:26 AM, minnale <[EMAIL PROTECTED]> wrote: > > Hi all, > 1) I have embedded protein into popcbilayer > 2) Energy minimisation > 3) Later added ions by usin

[gmx-users] step size too small

Hi all, 1) I have embedded protein into popcbilayer 2) Energy minimisation 3) Later added ions by using genion, 4) When I am trying to run minimisation its showing following sentences Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested p

[gmx-users] RE: anyone knows how to install grace?

> Gromacs 's web page proposes lesstif can also do as motif , so i downloaded > lesstif and installed it succefully , but grace prompted modtif not found > once again. > BTW: my OS is Fedora core 8 > > Can anyone give a good idear of installing grace.. I'm using grace on Ubuntu 8.04 and it runs e

Re: [gmx-users] tpbconv functionality

Hi Cesar, Not with tpbconv. You can do it with grompp, adding the .trr end .edr file you have as input and making sure that you don't generate new velocities and set unconstrained_start to yes. Cheers, Tsjerk On Sun, Jun 29, 2008 at 10:18 PM, Cesar Avila <[EMAIL PROTECTED]> wrote: > I found the