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 -9.999971e-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)
OK, that's what I expected you were doing - truncating the output and
not rounding appropriately. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic again -
I've updated it to deal with this issue more explicitly.
Mark
On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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 ]
; Name nrexcl
Protein_chain_A 3
=====================
error:-
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 23220 of the 23220 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20092 of the 23220 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1987
Fatal error:
No such moleculetype LIG
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
You have to make an attempt to solve your own problems :-) We have
better things to do than oversee every move you make. Follow that
link and read about this issue.
Mark
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
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