x27; '14447
All occupancies are one
Opening force field file
/home/dsarath/Utilities/share/451//amber99sb.ff/atomtypes.atp
Atomtype 1
---here pdb2gmx hangs
Best Wishes,
Sarath
Sarath Chandra Dantu
Computational Biomolecular Chemistry
Max Plan
-0.1180028
LP1LP -0.1100029
LP2LP -0.1100030
On Fri, Dec 3, 2010 at 4:40 PM, Justin A. Lemkul wrote:
>
>
> Sarath Chandra wrote:
>
>> Dear Gromacs users,
>>
>>
>> I have a nitroxide radical with lone pairs o
On Fri, Dec 10, 2010 at 12:16 PM, Jon Kapla wrote:
> Hi,
>
> Since I upgraded gromacs to > 4.5 I can't use g_protonate the way I'm used
> to. The error I get is that it can't find ffgmx2 library files in current
> dir or GMXLIB.The problem, I guess, could possibly be that g_protonate
> has no
On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran wrote:
> Hello madam,
>
> The command id
>
> *csh* *md.csh
>
> *
Please paste your md.csh file and the error you get in detail.
> **As I see, there is no error in the command. All other commands are
> properly working (like eq.csh, em.csh etc ).
generate a
> seed
> -[no]glasbool no Do glass simulation with special long range
> corrections
> -[no]ionize bool no Do a simulation including the effect of an
> X-Ray
> bombardment on your system
&g
>
> Thanks for the quick reply,
>
> I have already done that, and GROMACS, in all other cases, knows it is
> DNA, as it automatically forms the bonds with other residues.
>
> it is only when it makes its index files that it doesnt know that my
> residue is DNA.
>
Did you make the change in residue
On 29 May 2011 14:45, wrote:
> Hi all..
> I want to ask if it is possible to restart the md run if due to power
> problem final md run not completed means initiating md from where is stop
> due to any reason?
>
You can supply the checkpoint file written out, by -cpi option to mdrun and
continue
I suppose you are writing a extr.pdb form g_anaeig. Try writing down extr.
xtc and load it onto a pdb/gro using vmd. Then it should not be a problem.
Best Wishes,
Sarath
> Did you make the molecules whole and removed jumps (in case of a multimer)
> prior to filtering?
>
> Cheers,
>
> Tsjerk
>
>
.gromacs.org/mailman/listinfo/gmx-users>
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On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA wrote:
> Hello
>
> I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic"
> as box with distance of 1nm b/w solute n box.
> Protein is going out of the box after equilibration step. Any solution?
>
>
The protein does not diffuse
On Wed, Dec 22, 2010 at 11:23 AM, shikha agarwal wrote:
> I am trying to simulate a theorical model of a membrane protein in explicit
> lipid bilayer membrane environment (DMPC or POPC), I have the pdb
> files of this protein and membrane , I have to topolies files this
> lipids (dmpc.
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