Re: [gmx-users] Lennard Jones spheres

Hi Mark, I just want make use of the volumes of the spheres to enlarge the pocket without the use of any ligands. Thanks in advance! Chiara On Feb 19, 2008 1:12 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Chiara Parravicini wrote: > > Hi gromacs users, > > > > I would like to add LJ spheres i

Re: [gmx-users] Re: gmx-users Digest, Vol 46, Issue 56

sudheer babu wrote: Thanks Mark for your valuable reply and suggestions. If once i use "grompp" command its not showing any specific atom, its showing generally atomtype NR , HC, CR1 not found. if we come to topic of forcefields, For lipids i didnt use any Force field due to popc.top and popc.i

RE: [gmx-users] Strange dgdl-value together with lincs

> Date: Fri, 15 Feb 2008 09:27:24 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Strange dgdl-value together with lincs > > Berk, > > here comes the topology for this run (vdw morph): > Its OPLSAA and the hydrogen

RE: [gmx-users] calculating B-factor

thanks for your reply.. but that command gives B-Factor by atom. Is it possible to get by residue... > From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] calculating B-factor> Date: Mon, 18 Feb 2008 12:46:43 +0200> > Hi,> > check out g_rmsf (options -oq, -q, -ox), rmsf

Re: [gmx-users] Re: gmx-users Digest, Vol 46, Issue 56

8 ; > > qtot > > 3 > > 373 C 41PHECD2163 -0.1 12.011 ; > > qtot > > 2.9 > > 374 HC 41PHEHD21630.1 1.008 ; > > qtot > > 3 > > 375 C 41PHECE1

回复： Re: 回复： Re: 回 复： Re: 回复： Re: 回复 � Re: [gmx-users] about using amb2gmx.pl

Dear sirs: Thank you for your advices! The problem has been wiped off ! David Mobley <[EMAIL PROTECTED]> 写道： I think I can probably shed a little bit of light here, although Mark is getting close in the last chapter of his e-mail. Basically, pdb2gmx works well for parameterizing proteins

[gmx-users] Re: gmx-users Digest, Vol 46, Issue 56

8 HC 41PHEHE21650.1 1.008 ; > qtot > 3 > 379 C 41PHE CZ166 -0.1 12.011 ; > qtot > 2.9 > 380 HC 41PHE HZ1660.1 1.008 ; > qtot > 3 > 381 C 41

RE: [gmx-users] Strange dgdl-value together with lincs

> From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Strange dgdl-value together with lincs > Date: Tue, 19 Feb 2008 11:20:14 +0100 > > > > > > > Date: Fri, 15 Feb 2008 09:27:24 +010

Re: [gmx-users] Lennard Jones spheres

Chiara Parravicini wrote: Hi Mark, I just want make use of the volumes of the spheres to enlarge the pocket without the use of any ligands. How about using a ligand with charges set to zero? Or that and tinkered-LJ parameters? Mark ___ gmx-users

[gmx-users] problem in hdb file

Dear GMX users, I want to prepare .gro and topology file starting from the .pdb file for a polyethylene chain , whose residue is not defined in .rtp, .hdb. and .tdb files. I have defined a new residue in ffoplsaa.rtp file as follows [ Eth ] [ atoms ] C1opls_136-0.1201 H1

Re: [gmx-users] problem in hdb file

Zuzana Benkova wrote: Hi Zuzana, Thanks for the clear description of what you are attempting to do. Eth 2 2 6 H1 C1 C2 +C1 2 6 H2 C2 C1 -C2 At this point I have to note that the presence of the last control atoms in this file has not

Re: [gmx-users] Strange dgdl-value together with lincs

Thanks, Berk I'm also quite sure, that this spike doesn't explain the deviations I see in adding up single DG contributions. Maybe I just bring it up once more: Assume, you take the interconversion of ethane to methanol in solvent in one step. You sample hardcore at 11 evenly spaced lambda v

Re: [gmx-users] Lennard Jones spheres

Dear Mark, thanks for your reply! I'll try to better focus my issue: my intent is to perform simulations similar to which described in some recently published papers in which cavities are expanded by means of LJ spheres, using methods called "pressure guided MD" or "active-site pressurization" (K

RE: [gmx-users] Strange dgdl-value together with lincs

There could be many problems at different points. One can't say much without having looked in detail at all the data. Methanol will strongly hydrogen bond to water. So you need to be very careful that you sample the process of (dis)appearing this hydrogen bond carefully, both in the 1 and 3 step p

Re: [gmx-users] Lennard Jones spheres

Chiara Parravicini wrote: Dear Mark, thanks for your reply! I'll try to better focus my issue: my intent is to perform simulations similar to which described in some recently published papers in which cavities are expanded by means of LJ spheres, using methods called "pressure guided MD" or

Re: [gmx-users] Loss of GTP in topology file.

> Hi, > I have added missing atoms to my pdb file through servers of WHATIF,when I > use the force field option then the following output comes in shell console: > Fatal error: > Residue 'GTP' not found in residue topology database > and the following files are created: > 2a5f.top 2a5f_A.itp 2a5

RE: [gmx-users] Strange dgdl-value together with lincs

Maik, This is just a hunch, but since you're turning charges on (instead of off) in the third step, maybe this is also a case of bug 175 (http://bugzilla.gromacs.org/show_bug.cgi?id=175). That is, if you're using PME for electrostatics. This bug has been fixed for the CVS version. Another "fix" w