[gmx-users] request

[Dinesh Pinisetty]

Hi all,
I have known about GROMACS last month by this you can make out how
new I am in this field.I have many questions to ask but first let me ask
one in this mail.
I started with the sample MD code given in
md.chem.rug.nl/education/mdcourse2004,its on lysozymes.The pdb file was
imported from PDB data base in this tutorial the pdb file imported was
1AKI.pdb,when I ran the code importing this as given in this site code was
running but when I changed the pdb file i.e when I import 1IWZ.pdb and try
to run the simulation I was getting an error in the first step itself i.e
when I was trying to create a topology and gromacs files.
error was as follows

FATAL error: Atom HA in residue LYSH1 not found in rtp entry with 13 atoms
while sorting atoms.Maybe different protonation state.Remove this hydrogen
or choose a different protonation state.Option -ignh will ignore all
hydrogens in the input.

When I tried to import another pdb file for DMPC 1SMZ.pdb and try to create
.top and .gro files I was getting the following error.

FATAL error: Atom HA1 in residue GLY1 not found in rtp entry with 5 atoms
while sorting atoms.Maybe different protonation state.Remove this hydrogen
or choose a different protonation state.Option -ignh will ignore all
hydrogens in the input.

When I tried import another pdb file for GLYCEROL I was getting the
following error

FATAL error:Atom A01 in residue NDPH1 not found in rtp entry with 56 atoms
while sorting atoms.

Please bear with me for typing such a long mail,I just want to be clear in
mentioning the errors to you all as I am a beginner I do not even know
whether these errors are simple .I am sorry if I am disturbing you by
typing such a silly mail if this mail not worthy.
Please someone help me out in this regard,I hope someone of you will bear
me and do the needful.
Thanks a lot in advance for all of you.

Thanking you,
Yours sincerely,
Dinesh.

[Oliver Lange]

Hi Dinesh,

you should use the option -ignh, when you import pdb files with pdb2gmx.
This options means that the hydrogens, named in a gromacs-unfriendly-way, are ignored.
pdb2gmx places hydrogens by itself, so you don't have to worry that you loose them.
If you want to control protonation of histidin residues use the option -his.

Greetings
Oliver

Post by Dinesh Pinisetty
Hi all,
I have known about GROMACS last month by this you can make out how
new I am in this field.I have many questions to ask but first let me ask
one in this mail.
I started with the sample MD code given in
md.chem.rug.nl/education/mdcourse2004,its on lysozymes.The pdb file was
imported from PDB data base in this tutorial the pdb file imported was
1AKI.pdb,when I ran the code importing this as given in this site code was
running but when I changed the pdb file i.e when I import 1IWZ.pdb and try
to run the simulation I was getting an error in the first step itself i.e
when I was trying to create a topology and gromacs files.
error was as follows
FATAL error: Atom HA in residue LYSH1 not found in rtp entry with 13 atoms
while sorting atoms.Maybe different protonation state.Remove this hydrogen
or choose a different protonation state.Option -ignh will ignore all
hydrogens in the input.
When I tried to import another pdb file for DMPC 1SMZ.pdb and try to create
.top and .gro files I was getting the following error.
FATAL error: Atom HA1 in residue GLY1 not found in rtp entry with 5 atoms
while sorting atoms.Maybe different protonation state.Remove this hydrogen
or choose a different protonation state.Option -ignh will ignore all
hydrogens in the input.
When I tried import another pdb file for GLYCEROL I was getting the
following error
FATAL error:Atom A01 in residue NDPH1 not found in rtp entry with 56 atoms
while sorting atoms.
Please bear with me for typing such a long mail,I just want to be clear in
mentioning the errors to you all as I am a beginner I do not even know
whether these errors are simple .I am sorry if I am disturbing you by
typing such a silly mail if this mail not worthy.
Please someone help me out in this regard,I hope someone of you will bear
me and do the needful.
Thanks a lot in advance for all of you.
Thanking you,
Yours sincerely,
Dinesh.
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[Dinesh Pinisetty]

Hi all,
I am able to run the simulations,I want to figure out diffusive
property.
I ran the practice simulations given in GROMACS tutor.I have run
for the mixture of methanol and water there I was able to figure out the
diffusive property by calling g_msd.There I got options as system,MeOH and
water its giving diffusivity values differently,If D value of MeOH was
given I assumed that its the value of methanol diffusivity in
water,similarly for water I thought its the diffusivity of water in
methanol,but I did not get what the diffusivity of the system mean,is it
the self diffusivity value of the mixture or anything?
I have run the simulation for DMPC how to figure out the diffusive
property of water through DMPC as such or self diffusivity of the
DMPC+water etc.If I am calling g_msd subroutine its showing the error as
FATAL error: topo1.tpr does not exist or so.
How to modify topo1.tpr file to fullmd.tpr or input .tpr etc and how to
figure out the diffusivity of the membranes in water etc.
Someone please let me know this as soon as you see this query.
Thanks a lot in advance,for help in this regard.

Thank you,
Dinesh.

[Dinesh Pinisetty]

Hi everyone,
I am very sorry to disturb you all again,I know that there should be
topol.tpr file but when I am running the simulation for DMPC the tpr files
present in the directory where input.tpr and fullmd_sol.tpr.Should I rename
one of them so that g_msd reads them and gives out the diffusivity values.
Is there any way to permanently sort out the problem so that code
automatically reads the tpr file and gives out the diffusivity values.
Thanks all of you in advance.

Thanking You,
Dinesh.

[Oliver Lange]

Hi Dinesh,

rename the file you used for the MD to topol.tpr or use the option
-s fullmd_sol.tpr to specify your own tpr -file.
The .tpr file is needed for many tools, so the easiest way is to have a topol.tpr in your
directory when you do analysing.

Oliver

Post by Dinesh Pinisetty
Hi everyone,
I am very sorry to disturb you all again,I know that there should be
topol.tpr file but when I am running the simulation for DMPC the tpr files
present in the directory where input.tpr and fullmd_sol.tpr.Should I rename
one of them so that g_msd reads them and gives out the diffusivity values.
Is there any way to permanently sort out the problem so that code
automatically reads the tpr file and gives out the diffusivity values.
Thanks all of you in advance.
Thanking You,
Dinesh.
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gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.

[Dinesh Pinisetty]

Hi all,
The error when I am calling methanol pdb file 1AMT.pdb is as
follows:

Fatal error: Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms
while sorting atoms.

Please help me to sort out this problem.
I also expect someone to sort out the problem who tried for Glycerol.What
functions will help me out to set these problems I tried using -una etc but
I was repeatedly getting same errors.

As no one is there to help out and I am new to this field I am troubling
you all,once I understand everything clearly I will no longer trouble you
all for simple things.

Thanks a lot for all of you.I earnestly request someone to help me out in
sorting this problem out.

Thanking you,
Yours sincerely
Dinesh.

[Maria Sabaye Moghaddam]

Thanks a lot Anton. For some reason *itp files
were not there. I re-ran pdb2gmx, and now it
works.


Best,
Maria.

Hello;
I am very new with gromacs. I am at the initial stages of

getting

a trihelix in water simulation going. I have generated the *.gro and
*.top files, but I don't know how to generate an *.mdp file. I

copied the

one from the "Getting Started" section, but I am getting error

messages

filename_A.itp : No such file or directory
filename_B.itp : " " " " "

This probably has nothing to do with your choice of mdp options. Your

.top

file refers to (several) .itp file(s), which apparently cannot be

found.

You mention that you generated your .top file, I assume that was using
pdb2gmx. pdb2gmx should have generated the corresponding .itp files in
addition to the .top file. Maybe you missed them when copying/moving

things

to a different place?
--
Groetjes,
Anton
_____________

[Maria Sabaye Moghaddam]

Hi Everyone;

I am getting an error message after running:
grompp -f name.mdp -p name.top -c name.gro -o name.tpr

as
processing coordinates...
Fatal error: number of coordinates in coordinate file (name.gro, 202)
does not match topology (name.top, 2548)

I noticed that P. Keymer had got a similar message on June 3rd, but I
couldn't find an answer to his/her posting on the website. Does anyone
why I am getting this message?

Thanks,
Maria.

[Xavier Periole]

Post by Maria Sabaye Moghaddam
Hi Everyone;
grompp -f name.mdp -p name.top -c name.gro -o name.tpr
as
processing coordinates...
Fatal error: number of coordinates in coordinate file (name.gro, 202)
does not match topology (name.top, 2548)

you have to check the name.top file and include 2346 atoms that are missing
compared to the name.gro. May be the solvent ??

XAvier
--
----------------------------------------------

Xavier Periole - Ph.D.

Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Tel: [phone]
Fax: [phone]
email: x.periole at chem.rug.nl
web-page: http://md.chem.rug.nl/~periole

----------------------------------------------

[Leonardo Giantini Trabuco]

Post by Xavier Periole

Post by Maria Sabaye Moghaddam
Hi Everyone;
grompp -f name.mdp -p name.top -c name.gro -o name.tpr
as
processing coordinates...
Fatal error: number of coordinates in coordinate file (name.gro, 202)
does not match topology (name.top, 2548)

you have to check the name.top file and include 2346 atoms that are missing
compared to the name.gro. May be the solvent ??

In that case, you may want to use the '-p' option of genbox, which
updates your topology when the system is solvated.

Leo