Hello everyone..
I have 2 do the simulation of protein and peptide complex.I want to ask as
for protein and ligand complex we have 2 create topology of ligand using
prodrg sever mostly.Now if ligand is peptide then I have 2 build the
topology of peptide using pdb2gx or anyother means?Looking
HI all ..while running pdb2gmx command .I am getting error Fatal error:
Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms
while sorting atoms .what this error mean and how can I rectify this
problem?plz help me.
--
[image: images[12]]
“Many Smiles Begin Because Of Another
structure. Now my question is that how
can i see or open the .rtp file of particular force field?
On Wed, Jun 29, 2011 at 5:24 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rashi parihar wrote:
HI all ..while running pdb2gmx command .I am getting error Fatal error:
Atom CT in residue TYR 314
I want to obtain solvent accessible surface area using g_sas command:
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full
command as i am getting error while running this command.thanx in
advance!!
how I will obtain three output files containing: area.xvg, resarea.xvg
and
thanx justin..my problem is that i do not know exactly the syntax of
command.i get to know about this command through this community only.i.e why
i want the full command?
On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rashi parihar wrote:
I want to obtain solvent
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?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the
thanx sarath 4r reply..can u expalin little bit more..I did not get from
mdrun -h.
On , Sarath Chandra Dantu dsar...@gwdg.de wrote:
On 29 May 2011 14:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run
Hi all .
I am using trjconv command to genrate the pdb structures..
trjconv_d -f md_0_1.trr -s md_0_1.tpr -o md_0_1.pdb -nice 0 -sep -skip
1000 -tu ns -b 1 -e 5000
error is comingFatal error:
reading tpx file (md_0_1.tpr) version 73 with version 58 program.
what is meaning of this error and
Hi all
I have an ligand having NI atom(Nickel) .Now problem is this when I am
running PRODRG server ,ligand topology can not be created and error is
coming
*unsupported atom type NI (atom 'NI2 ') in your coordinates*.now how
to overcome this problem? plz help me!!
--
[image: images[12]]
“Many
HI all..
I am doing npt of protein-ligand complex. Now in that error is comingPressure
scaling more than 1%. How can I overcome this problem?
--
[image: images[12]]
“Many Smiles Begin Because Of Another Smile . . . .
Regards,
Rashi
image004.jpg--
gmx-users mailing list
10 matches
Mail list logo