On 21/06/2011 4:33 PM, bharat gupta wrote:
So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-
Please search for help first.
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Mark
Step=1, Dmax
On 21/06/2011 4:15 PM, bharat gupta wrote:
I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr
I am getting a charge of -9.71e-01
Since the charge has to be in whole number, what shall I do in this
case. (The ligand that I am using is p
So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-
Step=1, Dmax= 1.0e-02 nm, Epot= 1.36889e+09 Fmax= 1.97591e+11, atom=
1248
Step=2, Dmax= 1.2e-02 nm, Epot= 5.46814e+07 Fmax= 3.57239e+09, atom=
972
Step=3, Dmax= 1
I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr
I am getting a charge of -9.71e-01
Since the charge has to be in whole number, what shall I do in this case.
(The ligand that I am using is phosphotyrosine)
On Tue, Jun 21, 2011 at 2:13
On 21/06/2011 3:03 PM, bharat gupta wrote:
Now I changed the .top file in this way and I am getting this error now :-
change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
;Include ligand topology
#include "PTR.itp"
[ moleculetype ]
; Namenrexcl
Protein_ch
Now I changed the .top file in this way and I am getting this error now :-
change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
;Include ligand topology
#include "PTR.itp"
[ moleculetype ]
; Namenrexcl
Protein_chain_A 3
=
error:-
On 21/06/2011 2:51 PM, bharat gupta wrote:
ok now I am doing the things again and here is the result of output of
each command till adding ions. At the time of executing the command
grompp for reading em.mdp file for ions.tpr generation, I am getting
the following error:-
Fatal error:
Syntax
ok now I am doing the things again and here is the result of output of each
command till adding ions. At the time of executing the command grompp for
reading em.mdp file for ions.tpr generation, I am getting the following
error:-
Fatal error:
Syntax error - File PTR.itp, line 7
Last line read:
'[
bharat gupta wrote:
Hi,
In addition to my last mail, I am also getting another error during the
minimization step. I made the changes in em_real.mdp file for my sytem
but its showing the error that "ource code file: readir.c, line: 1316
Fatal error:
Group PTR not found in indexfile.
"
I
Hi,
In addition to my last mail, I am also getting another error during the
minimization step. I made the changes in em_real.mdp file for my sytem but
its showing the error that "ource code file: readir.c, line: 1316
Fatal error:
Group PTR not found in indexfile.
"
also the charge on the system
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