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Respected sir,
While i am running the gromacs always i am getting the
error "Residue 'GNP' not found in residue topology database".Kindly tell me
the what the error means.
Suryanarayana Seera,
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Respected sir,
While i am running the gromacs software i am getting the
following error.Kindly tell me how to over come the error.
Fatal error:
Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms
while sorting atoms.
SURYANARAYANA SEERA,
PhD student
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gmx-
Respected Sir,
While i am running the gromacs software i am getting
the following error.Kindly knowing how to over come the error.
Fatal error:
Residue 'CCN' not found in residue topology database
SURYANARAYANA SEERA,
PhD student.
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gmx-users mailing listgmx-users@grom
Respected Sir,
While i am running gromacs software i am getting the
following error.Kindly knowing me how to over come the error.
Fatal error:
number of coordinates in coordinate
file (1cys_ion.gro, 99670)
Respected Sir,
While i am running the gromacs software to simulate
the protein i am getting the following error.
Fatal error:
Residue 'GNP' not found in residue topology database
Suryanarayna Seera,
PhD student.
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gmx-users mailing listgmx-users@gromacs.org
http://l
Dear all gromacs users,
I tried the grompp and i got the following error."number of coordinates
in coordinate file (4INS_b4ion.gro, 90396)
does not match topology (4INS.top,
90393)".
Is there any explanation why is this
happ
Dear all Gromacs users,
While i am running gromacs software i am getting the following syntax
errors.
Fatal error:
Syntax error - File 1AX8.top, line 7934
Last line read:
'## #include"ions.itp"'
I am unable to create _b4em.gro files
Is there any explanation why is this happening? I would aoor
-- Forwarded message --
From: Seera Suryanarayana
Date: Thu, May 17, 2012 at 12:07 PM
Subject: How to overcome syntax errors
To: jalem...@vt.edu
Dear Justin,
While i am running gromacs software i am getting the
following syntax errors.
Fatal error:
Syntax
DEar all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Topology include file "ion.itp" not found
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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gmx-users mailing listgmx-users@gromacs.org
http://lis
Dear all,
While i am running gromacs software i am getting following
error.Let me know how to over come that error
Fatal error:
number of coordinates in coordinate file (208L_ion.gro, 62283)
does not match topology (208L.top, 62293)
Suryanarayana Seera,
PhD student,
Hyd
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
--
gmx-users mailing listgmx-users@gromacs.
Dear all gromacs users,
While i am running gromacs software i am
getting following error.Let me know that error how to over come.
Fatal error:
moleculetype CU1 is redefined
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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gmx-users mailing listgmx-us
Dear all gromacs users,
I tried the grompp and i got the
following error.
Fatal error:
moleculetype CU1 is redefined.
Is there any explanation why is thid happening?
I would appreciate any help. Iam new in using MD and gromac in particular.
Suryanarayana Se
Dear all gromacs users,
I tried the grompp and i got the following
error.
Fatal error:
number of coordinates in coordinate file (1UZ9_ion.gro, 41103)
does not match topology (1UZ9.top, 41100)
Is there any explanation why is thid happening?
I would
Dear all gromas users,
While i am running the grompp after first
mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
I would appreciate any help.I am new in using MD and gromacs in particular.
Dear all gromas users,
While i am running the grompp -c 1UZ9_em.gro -p 1UZ9.top -o
1UZ9_b4pr.tpr -f pr.mdp after first mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
I would appreciate any help.I am new in using MD and
Dear all gromacs users,
while running the command "grompp -c
1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp" i am getting the
following error.
File input/output error:
pr.mdp
Dear all gromacs users,
I am new for MD and in particular using
gromacs software.I would like to learn basics of gromacs.Please tell me the
name of the manual which one is suitable for me.
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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gmx-users mailing
Dear all gromacs users,
While i am using the commond" pdb2gmx -f
4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and
errors.
Warning: Residue EME21 in chain has different type (Other) from starting
residue ALA1 (Protein).
Warning: Residue
Dear all gromacs users,
I tried the "grompp -c 3I40_ion.gro -p 3I40.top -o
3I40_b4em.tpr -f em.mdp" and i got the following error.
Option Filename Type Description
-f em.mdp Input
Dear all gromacs users,
While i am running gromacs software i am getting following error.Let me
know that error how to over come.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology.
Suryanarayana Seera,
PhD student,
Hyderabad,
I
Dear all gromacs users,
While i am running pdb2gmx commond i am
getting following error.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology.
I wont ignore the 22 missing atoms by using -missing commo
Dear all gromacs users,
I tried the grompp and i got the following error.
Fatal error:
moleculetype CU1 is redefined.
Is there any explanation why is thid happening?
I've checked [moleculetypes] in topology files and there are not duplicated.
I would appreciate any help. Iam new in using
Dear Mark,
What type of file i have to check for missing of atoms.
Thanks and regards.
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Dear all gromacs users,
While i am running pdb2gmx commond i am
getting following error.
Fatal error:
incomplete ring in HIS231
Kindly tell me how to overcome this error and how to
Dear all gromacs users,
I have 1VZV.pdb file, in that file HIS231
has incomplete ring as N atom is missing.Can i add N atom to the .pdb file
if possible how can i add that atom to .pdb file.
Suryanarayana Seera,
PhD student,
India.
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gmx-users mailing listg
Dear all gromacs users,
After added the counter ions to the top
file and further i used 'grompp' commond,i got the following error.
Fatal error:
moleculetype CU1 is
redefin
Dear all gromacs users,
While running the grompp commond after
addition of counter ions i am getting the following error.
Fatal error:
number of coordinates
in coordinate fil
Dear all gromacs users,
While i am running the commond "mdrun -v
-deffnm em" iam getting the following error.
Fatal error:
Domain decomposition does not
support simple neighbor searching, use grids
Dear Justin sir,
I am simulating a protein 1AKI.pdb which is example of
your tutorial.I am doing simulations as your tutorial.I didnt get any
errors upto the commond "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p
topol.top -o em.tpr".After this as your tutorial i used the common
Dear all gromacs users,
I am doing moleculer dynamics by using gromacs
software.I got the following error after using the commond" mdrun -deffnm
nvt".
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not w
Dear all gromacs users,
While i am running the commond "trjconv
-f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500" i am getting
the following warning.
WARNING no output, last frame read at t=10
Kindly tell me how to overcome this error.
Suryanarayana Seer
-- Forwarded message --
From: Seera Suryanarayana
Date: Fri, Jun 15, 2012 at 1:38 PM
Subject: Regarding error.
To: gmx-users@gromacs.org
Dear all gromacs users,
While i am running the commond "trjconv
-f 1AKI_full.trr -s 1AKI_b4full.t
Dear all gromacs users,
While i am running the commond "mdrun
-deffnm nvt" i am getting the following error.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in
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