Dear users,
I have to complete my topology file and there is sulfate(SO4(-2)) in pdb file.
But I don't know how can I complete this file with oplsaa forcefield. I can't
find so4 in ffopls.tpr file. I would really appropriate if you could do this
for me.
thank you
Dear users,
I have a question about vdwtype. My question is if I use vdwtype=shift in
nvt.mdp file:
; Neighborsearchingns_type = grid ; search neighboring
grid celsnstlist = 5 ; 10 fsrlist= 1.0
; short-range neighborlist cutoff
of gromacs
manual (v4.0)/
-Gaurav
On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund er...@xray.bmc.uu.se wrote:
you zou skrev:
Dear users,
I have a question about vdwtype. My question is if I use vdwtype=shift in
nvt.mdp file:
; Neighborsearching
ns_type = grid ; search neighboring grid cels
Hi again,Thank you, I added missing atoms with emacs, but my question is this
ring doesn't have to be complete and if I add missing atoms with HIS680's name,
I change its structure. Is it true?
Hi Users,
I have a .pdb file, in this file when I want to use pdb2gmx command
there is this error
Hi everyone,
I have one question about topology, If I want to write topology by hand, how
can I write pairs and dihedrals without mistakes? Is there any free softwares
to use?
Thank you
_
Hi Users,
I have a .pdb file, in this file when I want to use pdb2gmx command there is
this error massage:Fatal error:Incomplete ring in HIS680
this aminoacid is not complete in general, I don't know how can I complete this
such that I don't add HIS for complete? Please give me a hint.
Thank
Hi everyone,
I had a .pdb file that was drug_enzyme complex. Drug was GOL(Glycerol) and I
wrote topology file by hand but now when I run grompp command I have this
error:Fatal error:Syntax error - File ffoplsaabon.itp, line 4Last line read:'[
bondtypes ]'Invalid order for directive bondtypes
Hi again,Sorry, in REMARK 470 there is:REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE
MISSING ATOMS (M=MODEL NUMBER; REMARK 470
Hi,Which tool(s) is/are useful? I don't have any idea for this problem.Thank you
you zou wrote:
Hi again,
Sorry, in REMARK 470 there is:
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN
Hi everyone,
I have one simple question. I don't know is there any different between OPLS-AA
forcefield and OPLS-AA/L forcefield? I think these are different but when I use
pdb2gmx tool there is no OPLS-AA forcefield to choose.
Thank you
Hi everyone,
I have one question about adding atoms that are missing in residue. This atom
is OG in SER amino acid. I don't know how can I add this atom to my residue. If
I have to add this atom manually how can I find coordinates of that? Or If
there is server or software to do this I will be
-atom structure.
-Justin
Thanks,
you zou wrote:
Hi again,
Sorry I confused you with my question. My question is How can I make .gro
file and .top file from
drug.pdb (that removed from drug-enzyme.pdb)?
If I can use x2top command I will make .top file just, is it true? I think
.gro
.pdb, How can it do
this, because number of atoms are different(Which command I have to use?). If
can't handle it how can I add Hydrogens to drg.gro?Thanks,
you zou wrote:
Hi again,
Sorry I confused you with my question. My question is How can I make .gro
file and .top file from drug.pdb
a forcefield type for 6 out of 24
atomsI don't know how can I adjust this error.I have one more question again,
this command give me a top file, if I want gro file of this pdb (drug that has
removed from drug-enzyme complex) how can I do that?
you zou wrote:
Dear Users,
I have one question about
command I will miss
something, is it true?Thank you again
you zou wrote:
Hi Justin,
Thank you for your help, But when I run x2top command there is one error
that is:
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top
Dear Users,
I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to
use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to
use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too,
or not?If I can't use this server, how can I make
Hi All,
I send you an email that now I want to remove/delete that but I do't now.my
question is how can I remove my email?
Thank you
_
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