[gmx-users] adding new lipid into /charmm27.ff/lipids.rtp

Dear All, Hi! I 'm using Charmm-gui to generate an empty membrane pdb and toppar, i managed to get the charmm topology from toppar directory. With that, I'm trying to put additional lipid topology from charmm-gui into /charmm27.ff/lipids.rtp (gromacs4.5.4) for my empty membrane. But with pdb2gmx,

Re: [gmx-users] Problem in equilibration for membrane system

e older version? is there any bugfix fot this? please help. regards, Bing On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham wrote: > Bing Bing wrote: > >> Dear All, >> I'm running the protein complex with POPC system. NVT (100ps) and NPT >> (200ps) were done with restra

[gmx-users] Problem in equilibration for membrane system

Dear All, I'm running the protein complex with POPC system. NVT (100ps) and NPT (200ps) were done with restraint on the protein follow by 1000 ps of NPT without restraint on protein. The trajectory was checked in term of pressure, potential, area per lipid were checked and everything seems ok (

[gmx-users] Problem with NPT equilibration

n also), it stop with Range checking error, whereby the ci value exceeded the ci cutoff. it is suggested that the minimzation might not done properly. But the minimization were converged in both stages. Is there anything i missed out here? Please advice.Thanks in advan

[gmx-users] invalid angle type 0

Dear all, I 've prepared POPC and protein with ffG53a6 forcefield. I've also built the ligand in the protein with ffG53a6, but it is not working. Many atom types in the ligand which i work on is not found in ffG53a6*.itp but if i change the forcefield to ffgmx, it work fine. I have tried to add-i

[gmx-users] using editconf to duplicate membrane

Dear all, I want to extend the membrane into 512 POPC with the starting structure of 128 POPC. I 've used :- editconf -f xxx.pdb -scale 2 2 1 -o zzz.pdb. I noticed that the pdb file that generated by editconf have only 1 set of 128 popc. Using vmd, the extended structure is in pieces, the no bond b

Re: [gmx-users] problem in g_order

Dear Erik, oo.i will be more meticulous next time. It works. :) thanks again. Regards, bing On Thu, Jul 2, 2009 at 9:38 PM, Erik Marklund wrote: > I see one typo. See below. > > Bing Bing skrev: > >> Dear all, >> I had created 3-21 group of sn1 chain for order

[gmx-users] problem in g_order

Dear all, I had created 3-21 group of sn1 chain for order analysis. I have issued:- make_ndx_d -f md_0_1.tpr -o sn1.dx > a C15 Found 128 atoms with name C15 3 C15 : 128 atoms > a C16 Found 0 atoms with name C16 Group is empty > a C17 Found 128 atoms with name C17 4 C1

[gmx-users] make index group

Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx > 15 & a Cxx |... >q i've got this error :- Group 15 not exist. I did not make index before I proceed with grompp for the mdrun, is it cause by this? thanks. Regards, bing _

Re: [gmx-users] Lipid bilayer moved apart

es with semi-isotropic > pressure coupling, though I am not sure what is the cause of the error you > are getting with NPT and LINCS. > > Regards, > -Shay > > > Quoting "Bing Bing" : > > Dear All, >> I'm simulating a empty membrane (128POPC +

[gmx-users] Lipid bilayer moved apart

Dear All, I'm simulating a empty membrane (128POPC + 2460 water) , the structure obtained from Tielemen's website. Thanks for the help from Justin and Mark, the structure had minimized and stop at 217steps Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. Improper Dih

[gmx-users] Problem in energy minimization for a empty membrane system

Hi! Thanks a alot for all the suggestions i've got from Justin and Mark. I found out that i actually deleted the box information from the starting structure PDB. Once i put it back, It worked. However, it stopped with this message. Stepsize too small, or no change in energy. Converged to machine p

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Does this mean that I'm suppose to throw away the water from the starting structure and resolvate it again? thanks again. regards, Bing On Tue, Jun 23, 2009 at 11:28 PM, Justin A. Lemkul wrote: > > > Bing Bing wrote: > >> Thanks for reply. >> I've used editconf

Re: [gmx-users] Problem in energy minimization for a empty membrane system

nt is require in another system (membrane+protein), i wanted to test it out in the this smaller systme before using it in the complete systme.However, it failed. Thanks in advance regards, bing On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul wrote: > > > Bing Bing wrote: > >> H

Re: [gmx-users] Problem in energy minimization for a empty membrane system

because the starting structure come together with water. I'm not sure this is the correct way of doing it. Please advice. Thanks in advance. Bing On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul wrote: > > > Bing Bing wrote: > >> Hi! I'm a postgraduate student

[gmx-users] Problem in energy minimization for a empty membrane system

Hi! I'm a postgraduate student from Malaysia and currently facing energy minimization problem for my membrane system. I'm trying to perform energy minimization for an empty POPC membrane with position restraint on the lipid. Minimization stop due to inf Fmax. And I noticed that in the log file as b