[gmx-users] Water near protein

within 2.0 A on the Y axis. What command could I use for doing this? If not, is there any way that this can be done? Thanks very much Ashutosh Jogalekar Modeling Laboratory Chemistry Department Emory University ___ gmx-users mailing listgmx-users

[gmx-users] Chain merging problem (pdb2gmx)

g the chains together. Since they are actually separate in reality, this is causing many problems, not the least of which is that the charge on the system is being cited as +1, when it should be +3. What should I do to get rid of this problem? Thanks Ashutosh Jogalekar Emory Unive

[gmx-users] LINCS deviation

get rid of the problem? dt= 0.002 nsteps= 1 constraints= all-bonds tau_p= 1.0 Thanks Ashutosh Jogalekar Emory University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't pos

Re: [gmx-users] Unnatural amino acid problems

Hello Mark Thanks for your comments. I realise that putting in zeros would not give me a good model. That's why I am putting in parameters in the .top file based on the atom types, which I get from the ffoplsaabon.itp file. But the distortion still persists, and in fact sometimes gets wors

[gmx-users] Unnatural amino acid problems

st 90 from its normal value of about 109. Whatever the cause for this distortion is, why is it affecting only some PHG residues and not others? Thank you Regards, Ashutosh Jogalekar Emory University. ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] .top file format

XYZ That is, does the specific spacing matter for the .top file? Thanks very much Ashutosh Jogalekar Emory University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Continuum solvent

continuum solvent model to do this if I can. I could use another program, but then it may not be a 'controlled experiment' Thanks Ashutosh Jogalekar Emory University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

Re: [gmx-users] Not enough ref_t and tau_t values

sary. Note that this basically was the problem given in the last post about "Not enough ref_t and tau_t values". Cheers, Tsjerk On 3/16/06, X.Periole <[EMAIL PROTECTED]> wrote: On Wed, 15 Mar 2006 17:21:52 -0600  Ashutosh Jogalekar <[EMAIL PROTECTED]> wrote:> I know this

[gmx-users] Not enough ref_t and tau_t values

, the error is showing up again and again. The top file also has a row only for protein and solvent. Help would be gladly appreciated as I cannot think of any reason since all the files look ok. Thanks very much Ashutosh Jogalekar Emory University

[gmx-users] Problem with phenylglycine MD

can I get the parameters for these dihedrals? Help will be really appreciated since I am stuck with this problem for days! Thanks Ashutosh Jogalekar Emory University, Atlanta, GA USA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/m

[gmx-users] Phenylglycine parametrization in OPLS

the C CA H angle is getting highly distorted). What can I do to remedy this? Thanks very much Ashutosh Jogalekar Emory University Chemistry Department ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Segmentation fault

Well, the log file says that the protocol is dying even before it starts the MD...so it stops right after it says 'Initializing LINear Constraint Solver' after which it displays the segmentation fault. Thanks Ashutosh On Mar 6, 2006, at 1:30 PM, Mark Abraham wrote: Ashutosh Jogal

Re: [gmx-users] Incorrect .top file numbering

are 7 strands of the peptide which form a sheet. Seven such sheets in turn are stacked on top of each other. This is the system I want to do MD on. I did use -merge in the pdb2gmx conversion. Thanks Ashutosh On Mar 6, 2006, at 1:37 PM, Mark Abraham wrote: Ashutosh Jogalekar wrote: I am trying to

[gmx-users] Incorrect .top file numbering

instead of 4, and after that, all the others are numbered successively. Why is this happening? Thanks Ashutosh Jogalekar Emory University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don&#

[gmx-users] Segmentation fault

tly to a specific source for the problem; on the other hand, there must be some specific source. So I was wondering whether anyone else has fixed this problem in a particular manner. I checked my input and everything seems to be ok at first sight. Thanks very much Ashutosh Jogalekar Emory

[gmx-users] Unnatural amino acid MD

ice for my amino acid, which is phenylglycine. But the ones that the program is asking me to put in seem to correspond to quite obscure atom combinations. Is this a problem with gromacs, or with the OPLS force field that I am using? Thanks Ashutosh Jogalekar Emory