On 7/18/14, 6:38 AM, RINU KHATTRI wrote:
hello every one
i am still in minimization step i thing i notice is -DSTRONG_POSERES is not
working even i added DSTRONG_POSERES in topology file
Because you've made a typo. -DSTRONG_POSERES will not trigger the STRONG_POSRES
block.
-Justin
i simpley used DPOSERES it workks in log file value is there
Energies (kJ/mol)
Bond G96Bond Angle G96Angle Proper Dih.
9.72432e+02 6.12232e+02 8.77917e+03 3.71444e+03 7.92883e+03
Ryckaert-Bell. Improper Dih. LJ-14 Coulomb-14 LJ (SR)
3.99236e+03 1.80953e+03 4.62776e+03 6.46567e+04 -1.53213e+04
Coulomb (SR) Coul. recip. Position Rest. Potential Pressure (bar)
-3.95141e+04 -1.46181e+05 4.32569e+02 -1.03490e+05
0.00000e+00
still protein is out
inflated.gro is ok but minimization step it is out
kindly help
On Fri, Jul 18, 2014 at 1:04 PM, RINU KHATTRI <nickname.mi...@gmail.com>
wrote:
hello justin images can not be sent by this email address (gmx--) i am
helpless how can i send it to you (protein is out side the lipid membrane )
thank you
On Fri, Jul 18, 2014 at 1:01 PM, RINU KHATTRI <nickname.mi...@gmail.com>
wrote:
hello gromacs users
i saw my em.log file after minimization no position restrain term is
there even i used -D flag
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef -DSTRONG_POSRES
#include "strong_posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef -DSTRONG_POSRES
#include "backbone_posre.itp"
#endif
; Include ligand topology
#include "drag.itp"
; Ligand position restraints
#ifdef -DPOSRES_UNK
#include "posre_UNK.itp"
#endif
; Include POPC chain topology
#include "popc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000000 1000000 1000000
2 2 1000000 1000000 1000000
3 3 1000000 1000000 1000000
#endif
; Include topology for ions
#include "gromos53a6.ff/ions.itp"
this my topology how can i put position restrain
minim.mdp
define = -DSTRONG_POSRES -DSTRONG_POSRES -DSTRONG_UNK
kindly help
On Thu, Jul 10, 2014 at 10:46 AM, RINU KHATTRI <nickname.mi...@gmail.com>
wrote:
hello every one
ohk i havbben pasted UNK portion from old files because it is still
missing in system.gro now after running minimization i got new error old
problem has resolved
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f minim.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c system_inflated.gro Input Structure file: gro g96 pdb tpr
etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o confout.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with
virtual
sites
-maxwarn int 2 Number of allowed warnings during input
processing. Not for normal use and may
generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions
without
defaults to zero instead of generating an
error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 813 of the 2346 non-bonded parameter combinations
ERROR 1 [file topol.top, line 22752]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 3 bonded neighbours molecule type 'POPC'
NOTE 1 [file topol.top, line 24831]:
System has non-zero total charge: 14.788998
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
There was 1 note
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
1388
Fatal error:
There was 1 error in input file(s)
kindly help
On Thu, Jul 10, 2014 at 10:17 AM, RINU KHATTRI <nickname.mi...@gmail.com
wrote:
hello gromacs users
ohk justin but if unk is deleted then how to put it back in
system_inflate.gro
On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
hello every one
I am working on complex with popc membrane i did
perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5
area.dat
after this step minimization
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
i got error
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 10224)
does not match topology (topol.top, 10245)
i have been removed 6 lipid molecules in my topology file according to
output i got one thing new in my system_inflate.gro file the written
displayed atom is 10224 but after counting it is 10536 so if i
correct it
difference is more
I don't know what this means, but the number of atoms that grompp is
finding is going to be correct.
in topology file [molecule]
protein chain 1
UNK 1
POPC 122
how to resolve it
I would venture a guess that UNK has 21 atoms. I don't know that
InflateGRO handles arbitrary molecules, so it may have gotten deleted upon
inflation. Check system_inflated.gro; it will be very obvious if it is
missing.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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