[gmx-users] Re: atoms jumps from its native position in protein

technical term to describe that. i am not sure where i am making mistake. could any one suggest this how to tackle this problem. thanks Parthiban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] Re: ProDRG error

Atomtype NR not found (while using G43a1) the small molecule was derived from pubchem and conformation was converted using Maestro with proper charges and EM. Thanks Parthiban. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Re: Problem in Disulfide Bond

db2gmx itself. is >> there any other way to fix it. >> > > Previously you said the bond was strained after EM. pdb2gmx is not capable > of straining a bond. > > Be sure you are not looking at "bonds" generated via heuristics in some > visualization program. I

[gmx-users] Re: Problem in Disulfide Bond

er way to fix it. but in gendral the molecule is free from strains. > >> also i have tried by editing specbond.dat as well but of no use. > > In what way? Have you seen the information at: > > http://www.gromacs.org/Documentation/File_Formats/specbond.dat > i tried t

[gmx-users] Re: gmx-users Digest, Vol 81, Issue 126

er way to fix it. but in gendral the molecule is free from strains. > >> also i have tried by editing specbond.dat as well but of no use. > > In what way? Have you seen the information at: > > http://www.gromacs.org/Documentation/File_Formats/specbond.dat > i tried t

[gmx-users] Re: Problem in Disulfide Bond

which did not worked at all. also i have tried by editing specbond.dat as well but of no use. can any one share/discuss some ideas how to fix this. reg's, Parthiban. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] Re:Indexing specific atoms

exed file with this, but the graph displays a wrong answer. thanks In advance. Parthiban. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)

[gmx-users] MD with bilayer

Hi I have constructed the bilayer with protein molecule in VMD. Can any one tell how to start MD from here. the initial step - pdb2gmx is not working for this complex(pdb+membrane) thanks in advance Parthiban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] pH studies

Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there any possibility in performing such work in gromacs. Thanks in advance Parthiban

[gmx-users] make_ndx help

Hi Anyone can please tell how to index 2 or more groups using make_ndx eg: 1 protein 12 sol 13 NA+ i tried giving >1&12, which shows that the "Group is empty" thanks in advance Parthiban ___ gmx-users mailing listgmx-

[gmx-users] Re: trjconv error

2008 09:53:02 +0200 >> From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] trjconv error >> To: "Discussion list for GROMACS users" >> Message-ID: >> <[EMAIL PROTECTED]> >> Content-Type: text/plain; charset

[gmx-users] trjconv error

Wassenaar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] trjconv error > To: "Discussion list for GROMACS users" > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Parthiban and Sundar, > > Did you

[gmx-users] trjconv error

hi all i can able to get .trr file after running md for 10 hrs but i cannot able to get the .trr to .xtc file which gives out the following error. can anyone guess, what type of error is this, & how to resolve it.. Parthiban & Sundar

[gmx-users] g_hbond output analysis

he -num option for g_hbond run. since i new to gromacs i cannot > able to interpret the output form. it comes in 3 columns with the first > column indicating the frame, i dont know about the remaining two columns > > Kindly suggest > > Parthiban & sundar > > > > ---

[gmx-users] g_hbond output analysis

hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns Kindly suggest Parthiban & su