[gmx-users] ATB server (charge assign)

[elham tazikeh]

Dear Justin
thanks for your good advise
as you're mentioned, i must include necessary file next to other force
field files in my directory
my version of gromaces is 4.6.5, and my force field is gromos 53a6

1-concerning below message, which ones is appropriate for me?
Gromacs3.x.x-4.0.x 53a6-54a7
or
Gromacs 4.5.x-5.x.x53a6

2-also, United-Atom PDB (original geometry)

will
be (*.pdb ) and needs to editconf to convert ( *.gro)...coordinate file
and
GROMACS G53A6FF United-Atom (ITP file)

will
be (*.itp)topology file

Is it right?

3-coud you please tell me, when i should get those files (*.pdb and *.itp)?
before include proposed new files in my directory or after that?

Regards
elham

Warning! This molecule contains non-standard atom types not included in the
standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the
internal GROMACS parameter files must be updated. These can be downloaded
using the link below. Instructions on where to place (and how to use) the
files are provided in the README file included in the archive.

Gromacs 3.x.x-4.0.x 53a6 - 54a7
 Gromacs
4.5.x-5.x.x 53a6

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[gmx-users] acetaminophen charges

[elham tazikeh]

Dear GMX usere

my problems is in the assigning the ligand charges in protein-ligand
simulation

(for instance :acetaminophen )

i acquired (*.itp ) file by PRODRG (after optimization by gaussian
software) and ATB server as below.

which one is appropriate to my MD simulation by gromaces:


*atom*

*By prodrg server*

*By ATB server*

CH3

0.013

-0.062

C

0.590

0.734

O

-0.493

-0.643

N

-0.716

-0.706

H

0.328

0.422

C

0.336

0.337

CR1

-0.150

-0.229

HC

0.171

0.176

CR1

-0.181

-0.286

HC

0.133

0.181

C

0.378

0.379

OA

-0.650

-0.590

H

0.405

0.445

CR1

-0.213

-0.286

HC

0.118

0.181

CR1

-0.181

-0.229

HC

0.124

0.176

in addition to, in ATB server, i saw this message in the page

(molid; 29980 or 26014):


Warning! This molecule contains non-standard atom types not included in the
standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the
internal GROMACS parameter files must be updated. These can be downloaded
using the link below. Instructions on where to place (and how to use) the
files are provided in the README file included in the archive.


Note: my force field was; gromos53A6

what is the meaning?

Regards
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[gmx-users] charge assign

[elham tazikeh]

Dear Justin
i really appreciate for your reply
i think my question wasn't clear. i prefer to express my problem again:

i'd like to accomplish protein-drug simulation by gromos force field and
before, docked my ligand on the protein (because,there wasn't the
crystallography file of this complex).
Now, to reach my destination, i eliminated ligand.pdb file from the end of
the complex.pdb and determined the charges of atoms by gaussian software by
mulicken method  (without optimization ), but the numbers of atoms in this
file and the files come from PRODRG server (the gromaces 87/gromacs
coordinate file .polar /aromatic hydrogens (*.gro) and the gromaces
topology (*.itp)) weren't the same.
 for this reason, i pasted the section of complex.pdb as lig.pdb in PRODRG
and achieved all formats of my ligand.
next, i saved the pdb file (polar/aromatic hydrogens) as ligand.pdb and
then give it to gaussian software to determination the charge of atoms.

Is it correct?
or
i should adding hydrogens to my ligand by another way?


Regards
elham
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[gmx-users] charge assign acetaminophen

[elham tazikeh]

Dear GMX users;
would you please help me about assigning the charges of my ligand
(acetaminophen) for entrance to simulation
i'd like to use the groups in aminoacids.rtp file in my force field
(gromos53a6) but i don't know how extract my charges
thanks
elham
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[gmx-users] protein simulation

[elham tazikeh]

Dear GMX users
i want to compare binding free energy between experimental and MD
computations
In experimental methods, we assumed that all atoms of a protein that
binding to ligand, butin MD simulations, we just assume the sections of
subdomain(s) that binds to ligand

Is this way correct to comparing the binding free energy have got from MD
with experimental analysis?

or in MD simulations, we must simulate all of subdomains in a protein
whatever bind to a ligand or not?

finally, suppose that there are for example 2 molecules of a ligand in a
pdb file of a protein (for instance in pdb:2i30 there are 2 molecules of SAL
we must suppose all of two molecules in pdb file or
once, simulate protein with ligand1 (SAL1) and after that simulate with
ligand 2 (SAL 2)?

Regards
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[gmx-users] trjcat

[elham tazikeh]

Dear GMX users
i ve simulated a system with 1500 steps in md.mdp file and every 3000
steps save the coordinations, thus we have 5000 frames
i know i should use *trjcat* for reduce my frames, but i dont know how?
for instance for reduction to 500 frames,
please guide me about that
regards
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[gmx-users] trjcat

[elham tazikeh]

Dear Thomas
i really apprciate for your advice
in
trjconv -dt NEW_TIME_STEP_IN_ps.
you mean place my new time and my  new steps of simulation instead of for
example 1500 steps
please clarify your mean
how i can resolve my problem for changing my steps from 15milion steps
(5000frame) to 500 frame
please write compelete command sentence by trjconv
regards
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[gmx-users] g_mmpbsa time

[elham tazikeh]

Dear users
i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps
for binding free energy computations by g_mmpbsa method in gromacs, my
computations took a long time
is it correct?
can i change my simulation time in *mdp* file for *tpr* production for
using in g_mmpbsa calculations or it s equal to  the time of my
siulation ???
regards
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[gmx-users] topology making by ATB/PRODRG

[elham tazikeh]

Dear GMX users
i d simulated a drug on a protein and in *ions.tpr* production process, i
ve got below error:



*Fatal error:number of coordinates in coordinate file (sol.gro,
29108) does not match topology (topol.top, 29116)*



i know ATB server is useful for molecules at most 40 atoms and my ligand
has 41 atoms,
* is there any version of ATB  can support of upper 40 atoms in the
ligand???*
Now, i cant resolve my error
i know the meaning of this error , but for topology making of my ligand,
 i used of ATB server and in ATB (*existing molecule section*)  , my
molecule has *8Hydrogen* fewer than the main structure (*total charge
was=zero*)
i added Hydrogen atoms to my ligand by *cmd* program and *submit* my ligand
to ATB server again for getting *lig.itp* correctly, but in ATB server, 3
files have been seen that all of them had non zero total charges (-1)
for this reason , i used of the topology file that existed in ATB server
Even by using PRODRG server, i ve got a topology file that had non zero
charges and COOH group assumed as COO- and 1H has been ignored...
and in PRODRG server , i ve got 1H fewer than the main structure

i really appriciate for any help
elham
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[gmx-users] No such moleculetype

[elham tazikeh]

Dear GMX users
i d simulated *Indometacin* on Human Serum Albumin by Gromacs 4.5
in *ions.tpr* process i encountered with the below error:


*Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987*



*Fatal error:No such moleculetype IMNFor more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
http://www.gromacs.org/Documentation/Errors*
i ve  checked my files (sol.gro  or topol.top) that seen added IMN
molecules to them

is there any relationship between my gromacs version with this issue or not

i really appriciate for any help
elham
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[gmx-users] adding hydrogens to pdb file

[elham tazikeh]

Dear GMX users
i want to *adding Hydrogens* to my lig.pdb (for making lig.itp file by ATB
server) in cmd program in Windowds, but i dont know the way of that?
i know the below command is used for that:
reduce.exe -BUILD lig.pdb  lig_h.pdb
but i cant do it in cmd program
i really appricite for any help
elham
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[gmx-users] binding free energy

[elham tazikeh]

Dear Users
for g_mmpbsa installation (by using source code and APBS 1.4 and gromacs
4.6.7)
after below command:
pdfco@pdfco-X:~/g_mmpbsa/build$ cmake -DGMX_PATH=/opt/gromacs \
 -DAPBS14=on \
 -DAPBS_INSTALL=/opt/apbs \
 -DCMAKE_INSTALL_PREFIX=/usr/local/bin/g_mmpbsa \
 ..
i saw:

-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/pdfco/g_mmpbsa/build

and after that by using make:
i ve got this messages:
Scanning dependencies of target energy2bfac
[ 10%] Building C object src/CMakeFiles/energy2bfac.dir/energy2bfac.c.o
Linking C executable energy2bfac
[ 10%] Built target energy2bfac
Scanning dependencies of target g_mmpbsa
[ 20%] Building C object src/CMakeFiles/g_mmpbsa.dir/main.c.o
[ 30%] Building C object src/CMakeFiles/g_mmpbsa.dir/energy_mm.c.o
[ 40%] Building C object src/CMakeFiles/g_mmpbsa.dir/InputPBSA.c.o
[ 50%] Building C object src/CMakeFiles/g_mmpbsa.dir/nsc.c.o
[ 60%] Building C object src/CMakeFiles/g_mmpbsa.dir/PbsaPrep.c.o
[ 70%] Building C object src/CMakeFiles/g_mmpbsa.dir/psize.c.o
[ 80%] Building C object src/CMakeFiles/g_mmpbsa.dir/radius.c.o
[ 90%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs14_main.c.o
[100%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs14_routines.c.o
Linking CXX executable g_mmpbsa
[100%] Built target g_mmpbsa
pdfco@pdfco-X:~/g_mmpbsa/build$ sudo make install
[sudo] password for pdfco:
[ 10%] Built target energy2bfac
[100%] Built target g_mmpbsa
Install the project...
-- Install configuration: 
CMake Error at src/cmake_install.cmake:50 (FILE):
 file cannot create directory: /usr/local/bin/g_mmpbsa/bin.  Maybe need
 administrative privileges.
Call Stack (most recent call first):
 cmake_install.cmake:37 (INCLUDE)

make: *** [install] Error 1
Also i ve got this error:

CMake Error: The source directory /home/pdfco/g_mmpbsa/build/ .. does not
exist.
Specify --help for usage, or press the help button on the CMake GUI.

i really apprciatefor any help
Sign in to reply
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[gmx-users] g_mmpbsa

[elham tazikeh]

Dear GMX Users
is there anyone to help me in g_mmpbsa using for binding free energy
calculation
i have questions about *.mdp files as polar.mdp or
for instance: what is the value of pdie in  protein-ligand combinations
i really appriciate for any help
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[gmx-users] Fwd: [g_mmpbsa] istallation Gromacs 4.6.7 Error

[elham tazikeh]

Dear Users
i work on gromacs 4.6.1 and ubuntu 14.04
for using* source code* installation for g_mmpbsa,

For Gromacs 4.6.7 installation , After using :

cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs -DGMX_GPU=off

i got this error:

CMake Error at cmake/FindFFTW.cmake:122 (message):
  The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared
  libraries.  Provide a different FFTW library by setting FFTWF_LIBRARY.  If
  you don't have a different one, recompile FFTW with --enable-shared or
  --with-pic.  Or disable shared libraries for Gromacs by setting
  BUILD_SHARED_LIBS to no.  Note: Disabling shared libraries requires up
to
  10x as much disk space.
Call Stack (most recent call first):
  CMakeLists.txt:923 (find_package)


-- Configuring incomplete, errors occurred!
See also /home/pdfco/gromacs-4.6.7/build/CMakeFiles/CMakeOutput.log.
See also /home/pdfco/gromacs-4.6.7/build/CMakeFiles/CMakeError.log.

how can i solve it?

i really appriciate for any guid
elham

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[gmx-users] Gromacs 4.5 or 4.6???

[elham tazikeh]

Dear Users
can i install both of versions of gromacs (4.5 and 4.6) on my ubuntu 14.04
or not?
my another question is;
can i install vmware along with ubuntu (consist of gromacs 4.5) on my
machine (my machine has ubuntu 14.04 and installed GRomacs 4.6 on it)
Regards
Elham
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[gmx-users] g_mmpbsa

[elham tazikeh]

Hi,
 I am new to g_mmpbsa and need some help. I have downloaded very latest
64bit binaries. My machine is 64bit and has ubuntu 14.04. There is problem
in binary, I am getting 'core dumped' error all the time. It says: Illegal
instruction (core dumped). For example, if I run a test
:- pdfco@pdfco-X:~/bindingEnergy$
g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../pbsa.mdp -pdie 2 -pbsa
-decomp
:-)  g_mmpbsa
(-:
Authors: Rashmi Kumari and Andrew Lynn
Contribution: Rajendra
Kumar
Copyright (C) 2013, 2014  Rashmi Kumari and Andrew
Lynn
   g_mmpbsa
is free software: you can redistribute it and/or modifyit under the
terms of the GNU General Public License as published bythe Free
Software Foundation, either version 3 of the License, or   (at your
option) any later
version.
  g_mmpbsa
is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of  MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE.  See the   GNU General Public
License for more
details.
 You
should have received a copy of the GNU General Public License   along
with g_mmpbsa.  If not, see http://www.gnu.org/licenses/.  ;

THIS
SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR   A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHTOWNER OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,   SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITEDTO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
OR  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
OF  LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDINGNEGLIGENCE OR OTH
ERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS  SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH
DAMAGE.
:-)  g_mmpbsa (-:
  Setting option -pdie more than once!Illegal instruction (core dumped)

please advise me as soon as possible
Regards
Elham
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[gmx-users] g_mmpbsa

[elham tazikeh]

Dear Leandro
i really appriciate for your help
i used of *Pre-compiled binary*
http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html#binary
for
my work and also i did them without -*pdie*, but i saw that error again.
should i change the number of -*pdie*  or not? i saw in Input Keywords for
Polar Solvation energy
http://rashmikumari.github.io/g_mmpbsa/Polar-solvation-input-parameters.html
that
*pdie*  was  = 4.i dont know why???
i really confused...
i ll be glad if i solve my error
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[gmx-users] increase the concentration of protein or drug

[elham tazikeh]

Dear GMX users
I d like to know about the way of increasing  protein concentration in
protein-ligand simulation.
Also increasing the drug concentration ( we know there are specific places
for ligand in the protein surface and we can not increase drug
concentration)
Unfortunately i still did not  get any compelete response.
I really appriciate if somebody can advice me in thus issue.
Regards
Elham
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[gmx-users] the study of concentration effect in gromacs

[elham tazikeh]

Dear Tsjerk

thanks for your advice

you mean , if i do my simulation in cubic box (1*1*1  nm3)...
Now, for twice of concentration, i should simulate for example in cubic box
(0.5*0.5*0.5  nm3)?
or for instance, i simulated on a system using *2i30* pdb file
(Aspirin+Salicilic Acid)
that including 2 molecules Aspirin with Salicilic Acid.
for increasing the concentration of substrate in this system, how can i
insert 2 molecules Salicilic Acid?i must insert the coordinate of Salicilic
Acid in my pdb file, again or not?

cheers
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[gmx-users] the study of concentration effect in gromacs

[elham tazikeh]

Dear All
i know for increasing ions in gromacs, we have to using GENION tool
but i dont know how increase or change * the protein* or drug concentration
in gromacs.
i ll really apriciate for any response
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[gmx-users] How can i save all run processes ...

[elham tazikeh]

Dear Mark/Leila
thanks for your reply
i knowing that for seeing all processes have done in my terminal page, i
must to use *history* tool
but *history* just give us main commands in my terminal page...i want to
see all processes with details (e.g. which group is choosed or the volume
of my box or...???)
overall, all details in my terminal page
regards
elham
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[gmx-users] preparing pdb file

[elham tazikeh]

Dear Gmx users
i have problem with making pdb(s) of proteins that have 2 chain or more.
my question is:

if in a protein, the active site for two of them (chains) are the same and
there is not any advantages one site to another site in chains...which one
is choiced?chain A or B?

for example: in pdb:2BXG (HSA+IBUPROPHEN); there are 2 chain and 3
sub-domains.
there are Ibuprophen (AC1 , AC2) molecules in domains 3,4,5.
i dont know which one of chains (A or B) is appropriate for study?
thanks a lot for any tip
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[gmx-users] choosing appropriate force field

[elham tazikeh]

Dear Justin
thanks for your help

i used of *ATB server* for making *.itp* file for SAL (salicylic acid), as
below:

[ moleculetype ]
; Name   nrexcl
_N4Y 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1OA1_N4YO101   -0.546  15.9994
2 H1_N4YH1610.469   1.0080
3 C1_N4Y C810.643  12.0110
4 O1_N4Y O91   -0.566  15.9994  ;  0.000
5 C1_N4Y C32   -0.221  12.0110
6 C1_N4Y C220.388  12.0110
7OA1_N4Y O72   -0.604  15.9994
8 H1_N4YH1520.437   1.0080  ;  0.000
9 C1_N4Y C13   -0.266  12.0110
   10HC1_N4YH1130.175   1.0080
   11 C1_N4Y C63   -0.049  12.0110
   12HC1_N4YH1430.140   1.0080  ;  0.000
   13 C1_N4Y C54   -0.201  12.0110
   14HC1_N4YH1340.141   1.0080
   15 C1_N4Y C44   -0.073  12.0110
   16HC1_N4YH1240.133   1.0080  ;  0.000
; total charge of the molecule:   0.000


here, i have a question:
in ATB server , there are 2 force field as default:* gromos 54A7 , gromos
53A6*
i did not see other force field,right?
for my simulation, can i choose *gromos43a1* or i have to choosing the same
force field (as ATB), i mean i must choose gromos 54A7?

on theother hand, Formats in ATB,were:
Gromacs
Gromos 11
Gromos 96

for my study, i choosed *Gromacs* as format in ATB , is it correct?

finally, for SAL molecule ; there is SAL in ATB as default, and i used of
it without loading of anywhere (same PRODRG)
is this correct?


at the end, shoul i  change *pdb* format (produced by ATB) to *gro* with
*editconf* tool in gromacs and then *copy* et the end of my  protein
coordinate file?
or
change my *complex.pdb* (get from RCSB) format to *coordinate.gro?*

i really appriciate for your advise

cheers
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[gmx-users] charge distriburion

[elham tazikeh]

Dear Justin
thanks for your replys

one of my most important problem is choosing correct pdb
in RCSB , there is not any pdb that consist of *Aspirin *+ HSA...and in
literature, using of *2i30* as pdb
my question is; should we use *docking software* for adding real Aspirin on
HSA or we can adding *ACE group to pdb file  (by hand*) or none of them?



finally, for pdb=2i30 , Atom section in my .itp file (produce by PRODRG0
was;

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OM 1  SAL O1' 1   -0.765  15.9994 ;'
 2 C 1  SAL C1' 10.354  12.0110 ;'
 3OM 1  SAL O2' 1   -0.765  15.9994 ;'
 4 C 1  SAL  C1 1   -0.027  12.0110
 5   CH2 1  SAL  C6 10.102  14.0270
 6   CH2 1  SAL  C5 10.101  14.0270
 7   CR1 1  SAL  C4 20.010  13.0190
 8   CR1 1  SAL  C3 20.010  13.0190
 9 C 1  SAL  C2 20.130  12.0110
10OA 1  SAL  O2 2   -0.191  15.9994
11 H 1  SAL  H2 20.041   1.0080

by advising your good  ideas, i saw in aminoacids.rtp for charge(s) and i
reached to below cherges:

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OM 1  SAL O1' 1   *-0.635*  15.9994 ;'
 2 C 1  SAL C1' 1*0.38*  12.0110 ;'
 3OM 1  SAL O2' 1  * -0.635*  15.9994 ;'
 4 C 1  SAL  C1 1*0*  12.0110
 5   CH2 1  SAL  C6 1*-0.1*  14.0270
 6   CH2 1  SAL  C5 1*-0.1*  14.0270
 7   CR1 1  SAL  C4 2*-0.1*  13.0190
 8   CR1 1  SAL  C3 2*-0.1*  13.0190
 9 C 1  SAL  C2 2   * 0.15*  12.0110
10OA 1  SAL  O2 2   *-0.548*  15.9994
11 H 1  SAL  H2 2   * 0.398*   1.0080


As showed in above table, the sum of chares are not still  Zero (even with
assuming H s ring)
please watch to them and give me help...

on the other hand, there are 2 molecules of SAL in pdb file that which one
have 10 atoms and in .itp file i achieved 11 atoms.is this correct?

Regards
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[gmx-users] farticle demanding about Small-Molecule Topologies

[elham tazikeh]

Dear Dr.Lemkul
would you please send me full text of your below article :

Practical Considerations for Building GROMOS-Compatible Small-Molecule
Topologies

unfortunately, i dont have accessible to full text of  this article
thanks a lot
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[gmx-users] pdb information

[elham tazikeh]

Dear GMX users
i d like to know about pdb information
for instance, when i defined concentration of an ion by genion (-conc),
gromacs added  ion(s) to my structure

Now, my question is:
in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation
in pdb file
i want to know about its concentration?
my mean is one Zn+2 ion equal *what concentration*?
regards
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[gmx-users] charge distribution

[elham tazikeh]

Dear Justin
thanks a lot for your response, your answers were very clear
As you said,for building blocks i cant use of protein force field and  i
have to get from the literature(s)
would you please recommend me some literature that i can use them?
cheers
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[gmx-users] pdb information

[elham tazikeh]

Dear Justin
i choosed *Cubic* box for amyloid beta peptide+Zn ion simulation
for this reason, my *volume* is defined
if i suppose that, Zn ion = 1 mol
its concentration will be calculated
my assumption is correct?

cheers
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[gmx-users] charge distribution

[elham tazikeh]

Dear Justin
i really appricite for your help
i want to tell all did work until now, again:


1.total charges in my topol.top was +2, then by genion, i added 2 CL to  my
comlex (HSA+Aspirin)

2.My .itp file (produce by PRODRG) was(consist of 11 atoms) :

[ moleculetype ]
; Name nrexcl
SAL  3
[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OM 1  SAL O1' 1   -0.765  15.9994 ;'
 2 C 1  SAL C1' 10.354  12.0110 ;'
 3OM 1  SAL O2' 1   -0.765  15.9994 ;'
 4 C 1  SAL  C1 1   -0.027  12.0110
 5   CH2 1  SAL  C6 10.102  14.0270
 6   CH2 1  SAL  C5 10.101  14.0270
 7   CR1 1  SAL  C4 20.010  13.0190
 8   CR1 1  SAL  C3 20.010  13.0190
 9 C 1  SAL  C2 20.130  12.0110
10OA 1  SAL  O2 2   -0.191  15.9994
11 H 1  SAL  H2 20.041   1.0080


with topology file and .itp file, after grompp (for produce nvt.tpr)
i encounted to below error :
*system has non-zero total charge : -0.61*


3.as yor re mentioned, Aspirin has 17 atoms.
for charge distribution, i used of QM (NBO calculation) and my results was:
1  C  -0.095205
2  C  -0.077566
3  C  -0.084684
4  C  -0.028579
5  C  -0.223106
6  C0.198041
7  H0.147099
8  H0.106100
9   H   0.101762
10  H  0.117238
11  C  0.443312
12  O  -0.318010
13  H0.247465
14  O  -0.341986
15  O  -0.318846
16  C0.312765
17  O  -0.320346
18  C  -0.281115
19  H0.136126
20  H0.139768
21  H0.139765

these are estimated for* 2-acetoxy benzoic acid *alone (i dont know , must
be calculate for complex HSA+Aspirin or Aspirin alone?)

4. on the other hand, i tried to search in *aminoacids.rtp* file for
*gromos* force field , but saw only charges for ACE group(other aminoacids
and some solvents) and i could not find out the charges of all atoms in
Aspirin molecule.

Overall, in your opinion, where is my problem?

i m looking forward to seeing your advise

cheers
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[gmx-users] core dumped

[elham tazikeh]

Dear users
when i simulated Aspirin on Human serum albumin (pdb: 2i30)
in equilibration process (NVT), i encountered with below message and my
simulation stopped. i dont know why?









*pdfco@pdfco-X:~/Aspirin$ tail nvt.job-nex int0   Number of
random exchanges to carry out eachexchange
interval (N^3 is one suggestion).  -nexzero or
not specified gives neighbor replica
exchange.-reseed  int-1  Seed for replica exchange, -1 is
generate a seed-[no]ionize  bool   no  Do a simulation including the
effect of an X-Raybombardment on your system*



*Reading file nvt.tpr, VERSION 4.6.5 (single precision)Using 1 MPI
thread[1]+  Segmentation fault  (core dumped) mdrun -v -deffnm nvt 
nvt.job*





my *NVT.mdp* content was:

title  = Protein NVT equilibration
define  = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md   ; leap-frog integrator
nsteps  = 10  ; 0.002 * 10 = 200 ps
dt  = 0.002  ; 2 fs
; Output control
nstxout  = 1000  ; save coordinates every 0.2 ps
nstvout  = 1000  ; save velocities every 0.2 ps
nstenergy = 1000  ; save energies every 0.2 ps
nstlog  = 1000  ; update log file every 0.2 ps
; Bond parameters
continuation = no  ; first dynamics run
constraint_algorithm = lincs  ; holonomic constraints
constraints = all-bonds  ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1   ; accuracy of LINCS
lincs_order = 4   ; also related to accuracy
; Neighborsearching
ns_type  = grid  ; search neighboring grid cells
nstlist  = 5  ; 10 fs
rlist  = 1.0  ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0  ; short-range electrostatic cutoff (in nm)
rvdw  = 1.0  ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME  ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4  ; cubic interpolation
fourierspacing = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = v-rescale
tc-grps  = Protein_SAL SOL_CL ; two coupling groups - more accurate
tau_t  = 0.1 0.1 ; time constant, in ps
ref_t  = 310  310 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl  = no   ; no pressure coupling in NVT
; Periodic boundary conditions
pbc  = XYZ
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel  = yes  ; assign velocities from Maxwell distribution
gen_temp = 300  ; temperature for Maxwell distribution
gen_seed = -1  ; generate a random seed



i really appriciate for your hint

regards
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[gmx-users] charge distribution

[elham tazikeh]

Dear gromacs users
i d like to know about charge distribution in .itp file that how can fix
the charge of atoms
for instance, i simulated Aspirin in Human serum albumin, and i want to
know about their charges
in an article charge distribution was as below, but in my .itp file
(aquired by PRODRG server) i had 11 atoms instead of 13 atoms
please help me how can fix partial charges?
thanks for any hint

Atom
numberAtom
TypeNameCharge
groupPartial
ChargeMass
--
1OMOL1−0.635 15.99942CCK10.27 12.0113OMOM1−0.635 15.99944CCJ20 12.0115CR1CI
20 13.0196CR1CH20 13.0197CR1CG30 13.0198CR1CF30 13.0199CCE30 12.01110OAOD40
15.999411CCB40.38 12.01112OOC4−0.38 15.999413CH3CA50 15.035
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[gmx-users] core dumped

[elham tazikeh]

Dear Justin
thanks for your advise
only my remained question is, if my problem was for my topology file (as i
recieved this error a few times: your topology file has non-zero charge =
 -0.61)
by editing my topology file (.itp file), can i going on my simulation?
please tell me, what is the best way for distribute the charges on a
molecule (Aspirin)?
thanks for your help
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[gmx-users] free energy problem

[elham tazikeh]

Dear Justin
thanks for your replys and your patient

i think my main  problem is the way of using of perl/shell scripts in your
tutorial (Free energy for methane)

my question is: for script using, i must be execute them by *(chmod +x
...) * and then use of this command (*perl write_mdp.pl
http://write_mdp.pl em_steep.mdp * or
*sh write_sh.pl http://write_sh.pl em_steep.sh*) ? are they correct?

in this tutorial, its up to us that choose of *perl scripts *or *shell
scripts* without any difference?right??

at the end, script files read from mdp files without any changes or
rep0lacing by values by us...is it correct?

best regards
elham
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[gmx-users] free energy question

[elham tazikeh]

Dear Justin
Your mean is, i should use:
perl write_mdp.pl em_steep.mdp
For creating *.mdp files for EM process per lambdas

And for producing for example nvt.mdp,i must write:
perl write_mdp.pl  nvt.mdp ?

Also for acheiving neccesary files for run process we need to shell files
...but i dont know about writing and accessing to job_*.sh?

Could you please advise me
Thank you
Elham
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[gmx-users] free energy for ethanol

[elham tazikeh]

Dear Justin
i really appriciate for your reply

i trying to follow this tuturial about free energy of ethanol:
*http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf
http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf*

there was* mklambda.sh* in that tutorial
when i used above command for creating different lambdas:
*sh mklambdas.sh run.mdp topol.top equil.gro*

i  will receive this error:
*mklambdas.sh: 12: Syntax error: ( unexpected*
how can i fix it?

about your tutorial (methane), you said , you must change some sections
i follow your tutorial but received empty files for every lambdas...
could you please send me some tutorials for practicing this issue (Free
Energy Calculation)?

best regards
elham
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[gmx-users] free energy calculation

[elham tazikeh]

Dear users
For calculating free energy of methan (in justin tutorial)
I changed important parameters instead of  the parameters in lambda=0  that
having in that tutorial
Is it correct?
Or i must create those files by this command:
Perl write_mdp.pl em_steep.mdp for every lambda?!

I did this way.but my received files were empty
Please help me
Regards
Elham
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[gmx-users] free energy of methan

[elham tazikeh]

Dear users
in attached *.mdp* file, if i replaced *init_lambda_state=0.05 , 0.1 , 0.15*
, ... instead of *0* for* lambda=0*
is correct?
i didnot see foreign lambda in this mdp file.where i include foreign
lambda???
regards
elham tazikeh

*mdp file for lambda=0*
; Free energy control stuff
free_energy  = yes
*init_lambda_state= 0*
*delta_lambda = 0*
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state012345678
910   11   12   13   14   15   16   17   18   19   20
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
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[gmx-users] error in free energy calculation

[elham tazikeh]

Dear Justin
when I am doing  this tutorial

*sh mklambdas.sh run.mdp topol.top equil.gro*

I got following error:

*mklambdas.sh: 12: mklambdas.sh: Syntax error: ( unexpected*


How can I fix this?


Best regards,

elham
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[gmx-users] perl script running

[elham tazikeh]

Dear users
how can i running perl script files in my linux ?

is this correct?
chmod +x  *.pl
perl ./ *.pl  *.xpm

thanks for your reply
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[gmx-users] scount.xvg analysis

[elham tazikeh]

Dear Justin
thanks for your reply
is there any script for my  problem?
i heard there is ss.pl file for this issue,but i don, t have it.
could u please help me?!
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[gmx-users] (no subject)

[elham tazikeh]

Dear users
i used of *g_saltbr* for Amyloid Beta Peptide with Zinc cation simulation
and aquired 3 outputs :min-min.xvg, plus-min.xvg , plus-plus.xvg

there are 5 salt bridges between His 6 , Glu 11 - His13 , Glu 11- His 14 ,
Glu 11- His 13 , His 14 and also between Asp 23 , Lys 28

in this issue, i can not use of above outputs and i dont know how analyze
those files?
please help me

Best Wishes
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[gmx-users] g_saltbr analysis

[elham tazikeh]

Dear users
i used of *g_saltbr* for Amyloid Beta Peptide with Zinc cation simulation
and aquired 3 outputs :min-min.xvg, plus-min.xvg , plus-plus.xvg

there are 5 salt bridges between His 6 , Glu 11 - His13 , Glu 11- His 14 ,
Glu 11- His 13 , His 14 and also between Asp 23 , Lys 28

in this issue, i can not use of above outputs and i dont know how analyze
those files?
please help me

Best Wishes
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[gmx-users] scount.xvg analysis

[elham tazikeh]

Dear Users
i,d like to have a figure , *residue numbers* vs* the percent of
alpha-helix, beta-sheet and other secondary structures*
but i can not plot them...
is there any way to solve my problem?
thanks for your favor
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[gmx-users] No such moleculetype ZN

[elham tazikeh]

Dear Justin/ *Dhanachandra *
*thanks for your reply*

*as you konw, i simulated Zinc cation on hGH protein*
*and received  an error in energy minimization  process in em.tpr
production(*grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr)*, as
below:*

*No such moleculetype ZN*

*in one hand, i checked my ions.itp file and saw there is no ZN ion in it,
but atp file in my choosed force field (opls) support ZN ion same CU ion
(about CU cation, i had not any problem)*

*on the other hand, by genion command, i could replace ZN ions instead of
sol (water) molecules, easily*

*i don,t know it,s related to my version pf gromacs 4.6.5 or not?*

*Regards*
*elham tazikeh*
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[gmx-users] No such moleculetype ZN

[elham tazikeh]

Dear Justin

Please ignore my previous questions.

I want to do 2 md simulations: 1) protein and Cu, 2) protein and Zn.
After checking

force fields in gromacs 4.5.3, I found oplsaa in which there are both
Cu and Zn ions

in atomtype.atp file. Then I used gromacs 4.6.5 (with opls force
field) to do md

simulations. I added ions to my system using genion command.


genion -s ions.tpr -o sol_ions.gro -p topol.top -pname CU -pq +2
-neutral -conc 0.025.

genion -s ions.tpr -o sol_ions.gro -p topol.top -pname ZN -pq +2
-neutral -conc 0.025.

In both cases, ions were added without problem. Then, I used

grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr

In case of protein and Cu, there is not problem. But, in case of protein
and Zn,

I encountered error: No such moleculetype ZN.

I checked ions.itp in opls force field in gromacs 4.6.5, I found, there are both

Cu and Zn ions in atomtype.atp file. But, there is only Cu in ions.itp file.

How to do md simulation of protein-zn system using gromacs 4.6.5.


Any help will highly appreciated.
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[gmx-users] (no subject)

[elham tazikeh]

Dear Users
I simulated Zinc ion on human growth hormone protein by Gromacs 4.6
and encountered with this message:

there are not molculetype for Zn

this sentence means I can not simulate this system on Gromacs 4.6 and have
to install version 4.5 on my system or not?

regards
elham tazikeh
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[gmx-users] genion

[elham tazikeh]

dear users
i studied on amyloid beta peptide with zinc cation and
i choosed 1ze9 as my pdb file
can i assume Zn without charge in  protein simulation alone,
or i have to using the amyloid beta peptide alone as pdb
for instance,1iyt???
best wishes
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[gmx-users] g_covar

[elham tazikeh]

Dear users
in my anslysis ,i did g_covar and encountered to this note:
(the fit and anslysis group are identical while the fit is mass weighted
and the analysis is not making the fit non
mass weighted)
is this important note or not?

thanks for your reply
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[gmx-users] pbc problem

[elham tazikeh]

dear gromacs users
i did simulate zinc and copper ion on human growth hormone protein
when i saw my md.gro and md.xtc files by VMD software
i found out my system isn,t in the box(cubic)
i tried to solve this problem by :

trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol

but there is this problem,again.
could you please help me
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[gmx-users] dssp installation error

[elham tazikeh]

dear gromacs users
when i run do_dssp program 4.5 and 4.6
i saw below error
plz help me

progran do_dssp, version 4.5.3
source code file:do_dsso.c, line: 521

fatal error:
failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A 
/dev/null2 /dev/null

best regards
elham tazikeh
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[gmx-users] protein simulation

[elham tazikeh]

Dear Justin
thanks for your quick reply
i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i
choose 1ZE9 as pdb my choice is correct or i have to pdb of protein without
cation for my work or can i delete zinc ion effect in that pdb? for force
field choosing ,i think Opls is appropriate for this simulation...isn,t it?
best wishes
elham
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[gmx-users] RMSD

[elham tazikeh]

Dear gromacs users

Can somebody tell me how to calculate the RMSD of the peptide conformation
relative to the NMR structure?

Best wishes
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[gmx-users] force field

[elham tazikeh]

Dear friends
who knows about force field choosing in zinc ion complex with amyloid beta
peptide protein???
i,m looking forward to your reply
thank you
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[gmx-users] force field

[elham tazikeh]

 Dear Justin
thanks for your quick reply
i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i
choose 1ZE9 as pdb
my choice is correct or i have to pdb of protein without  cation for my
work or can i delete zinc ion  effect in that pdb?
for force field choosing ,i think Opls is appropriate for this
simulation...isn,t it?
best wishes
elham
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