[gmx-users] HEME-cysteine gromacs simulation

[chris . neale]

You always need a correct topology. The main issue here is that you  
need to have correct parameters. Where did you get your heme and Fe  
parameters? Were you careful about the Fe state oxidation state? I  
suspect that most people use Amber because of their antechamber  
program, which seems like a brilliant idea even if it may overstretch  
it's own parameterization without letting you know. I have no specific  
advice for you here beyond saying that it is worth spending a month  
figuring out what parameters you should really be using (hint: why  
would you be using ffG43a1 if most others use Amber here? do you know  
something that they don't?). This will end up saving you time in the  
long run.


Note that ffG43a1 is the GROMOS forcefield, not the  GROMACS  
forcefield. It is unfortunate that many programs (Amber, Charmm,  
gromacs) have their own similarly named forcefield, but that does not  
mean that the forcefield must be used with the associated program.  
There are forcefields that are not associated with a program (OPLS)  
and programs that never developed their own force field (NAMD,  
Desmond, Tinker, LAMMPS), so it is perfectly ok for you to use the  
amber forcefield with the gromacs program.


Bottom line: read, read, read.

Chris.

-- original message --

I want to run a simulation with  heme group(cytochrome p450). i have  
made a 3-d structure model for a cytochrome p450 .I use the ffG43a1  
force field,someone told me that i need both suitable parameters for  
your desired force field, and then to construct a correct topology. I  
read lots of papers,but most of them used amber force field.Befor  
runing the gromacs molecular simulation,i define the heme group as a  
new residue in the .rtp files,following the required  
formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then  
define a new FE-S bong.


i run the simulation like this:

pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top  
-water spce

editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9
genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top
grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr
genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top  
file, delette em.tpr

grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr
mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr
grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr
mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log

 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with  
accelrys ds visualizer or sybyl,the atom FE was recognized as F  
(Fluorine)and the pdb miss the bonds between FE-S &FE-N,i add or  
delete a blank space befor or after the FE in the pdb file,it was read  
as iron(FE) again but still missing;when checking the .top file,there  
was a FE (both atom name and type)and formed the FE-S & FE-N bonds.


if i ignore the above things,go on the command ,when runing the em.mdp  
there is a tip that Steepest Descents failed converged to Fmax < 1000  
in 5001 steps.when run the pr.tpr,a error emerged as segment fatal  
error¡£


2 someone told me that i need both suitable parameters for your  
desired force field, and then to construct a correct topology. I read  
lots of papers,but most of them used amber force field.Does anyone  
known a paper with a gromacs force field for HEME group?


please help me how handle those problems,how can i go on the simulation?

the HEME-cysteine parameter in the rtp files,define themas a new  
residue.(is there any problems?)


[ HEME ]
 [ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2-0.1 2
   SG S-0.4 2
C C 0.38000 3
O O-0.38000 3
   FEFE 0.84700 4
   NANR-0.37000 4
   NBNR-0.42300 4
   NCNR-0.50400 4

 [ bonds ]
N Hgb_2
NCAgb_20
   CA Cgb_26
C Ogb_4
C+Ngb_9
   CACBgb_26
   CBSGgb_30
   SGFEgb_48
   FENAgb_34
   FENBgb_34
   FENCgb_34
   FENDgb_34

.
 [ angles ]
;  aiajak   gromos type
   -C N H ga_31
H NCA ga_17
   -C NCA ga_30
NCA C ga_12
   CA C+N ga_18
   CA C O ga_29
 ...
 [ impropers ]
;  aiajakal   gromos type
N-CCA H gi_1
CCA+N O gi_1
   CA N CCB gi_2
   FESGNAND gi_3
   FESGNANB gi_3
   FESGNBNC gi_3
   FESGNCND gi_3
  .
 [ dihedrals ]
;  aiajakal   gromos type
  .


ûÓйã¸æµÄÖÕÉíÃâ·ÑÓÊÏä,www.yeah.net




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Re: [gmx-users] HEME-cysteine gromacs simulation

[Mark Abraham]

?? wrote:

HI all:

I want to run a simulation with  heme group(cytochrome p450). i have made a 3-d 
structure model for a cytochrome p450 .I use the ffG43a1 force field,someone 
told me that i need both suitable parameters for your desired force field, and 
then to construct a correct topology. I read lots of papers,but most of them 
used amber force field.Befor runing the gromacs molecular simulation,i define 
the heme group as a new residue in the .rtp files,following the required 
formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new 
FE-S bong.

i run the simulation like this:

pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water spce   
editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9   
genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top  
grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr  
genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, delette em.tpr 
grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr  
mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr   
grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr  
mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log 


 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds 
visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss the 
bonds between FE-S &FE-N,i add or delete a blank space befor or after the FE in the 
pdb file,it was read as iron(FE) again but still missing;when checking the .top 
file,there was a FE (both atom name and type)and formed the FE-S & FE-N bonds.


Visualization programs have to use heuristics to guess where bonds are 
and what names occur for which atoms (HG1 might be mercury or the first 
hydrogen on a gamma carbon, NE might be neon or an epsilon nitrogen, 
etc.). Only if you are able to read in a .tpr (such as with ngmx 
distributed inside GROMACS) can you get any visual confirmation of what 
GROMACS thinks you have described in your topology. There is no 
standardized widely-used mechanism for including such information in a 
PDB file, and so such usage of a file is unreliable.



if i ignore the above things,go on the command ,when runing the em.mdp there is a 
tip that Steepest Descents failed converged to Fmax < 1000 in 5001 steps.when 
run the pr.tpr,a error emerged as segment fatal error??


Read the .log files as well. GROMACS almost never segfaults (except when 
subjected to buggy MPI libraries), and when it does it will normally 
write some diagnostic information to stdout or the .log file.



2 someone told me that i need both suitable parameters for your desired force 
field, and then to construct a correct topology. I read lots of papers,but most 
of them used amber force field.Does anyone known a paper with a gromacs force 
field for HEME group?


Sorry, I can't help there.


please help me how handle those problems,how can i go on the simulation?

the HEME-cysteine parameter in the rtp files,define themas a new residue.(is 
there any problems?)


Look at the results in ngmx to get started. Try generating a structure 
for some minimalist version of the heme group and get EM and MD to work 
on that first. If you reduce the complexity, you can eliminate potential 
sources of problems until you find the source.


Mark

[ HEME ] 
 [ atoms ]   
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2-0.1 2
   SG S-0.4 2
C C 0.38000 3
O O-0.38000 3
   FEFE 0.84700 4
   NANR-0.37000 4
   NBNR-0.42300 4
   NCNR-0.50400 4

 [ bonds ]   
N Hgb_2  
NCAgb_20 
   CA Cgb_26 
C Ogb_4  
C+Ngb_9  
   CACBgb_26 
   CBSGgb_30 
   SGFEgb_48 
   FENAgb_34 
   FENBgb_34 
   FENCgb_34 
   FENDgb_34   

.  
 [ angles ]  
;  aiajak   gromos type  
   -C N H ga_31  
H NCA ga_17  
   -C NCA ga_30  
NCA C ga_12  
   CA C+N ga_18  
   CA C O ga_29  
 ...   
 [ impropers ]   
;  aiajakal   gromos type
N-CCA H gi_1 
CCA+N   

Re: [gmx-users] error while executing grompp

[Mark Abraham]

Justin A. Lemkul wrote:


Your ffcharmm.itp file lacks a necessary line at the very top:

#define _FF_CHARMM

Without this line, grompp does not know which force field you are using, 
and hence everything breaks down when other .itp files are called.


On closer inspection, Chanchal's source at 
http://www.bioinf.uni-sb.de/RB/ is redistributing a not-fully-functional 
version of the results of my CHARMM conversion scripts. I believe such 
redistribution is not technically a breach of the GPL license under 
which I released those scripts (since my copyright extends to the 
scripts, but not to their results since I understand that these are not 
"derivative works"), but those files and the website don't acknowledge 
their origin. The pre-print journal article linked there does 
acknowledge my work suitably, however. I'll email them and ask for a 
suitable correction.


Mark


-Justin

Chanchal wrote:

Hi,
  Attached are the top and itp file I am using. Please help me to fix 
the problem.

Thanks
Chanchal


On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul > wrote:




Chanchal wrote:

Hi All,
  I have downloaded pdb file and required .top and .itp file
from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
simulation. Now when I execute the command
 grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal error:
[ file tip3p.itp, line 42 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section
"settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

Attached is the em.mdp file I am using. Please help me how to
solve this problem.


Please see here:


http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds 



The .mdp file is not the source of the problem; the topology is.  If
you need more help, you'll have to post the relevant section.

-Justin

Thanks
Chanchal






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-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] HEME-cysteine gromacs simulation

[郭建路]

HI all:

I want to run a simulation with  heme group(cytochrome p450). i have made a 3-d 
structure model for a cytochrome p450 .I use the ffG43a1 force field,someone 
told me that i need both suitable parameters for your desired force field, and 
then to construct a correct topology. I read lots of papers,but most of them 
used amber force field.Befor runing the gromacs molecular simulation,i define 
the heme group as a new residue in the .rtp files,following the required 
formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new 
FE-S bong.

i run the simulation like this:

pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water 
spce   
editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9   

genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top  

grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr  

genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, 
delette em.tpr 
grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr  

mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr   

grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr  

mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log 

 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds 
visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss 
the bonds between FE-S &FE-N,i add or delete a blank space befor or after the 
FE in the pdb file,it was read as iron(FE) again but still missing;when 
checking the .top file,there was a FE (both atom name and type)and formed the 
FE-S & FE-N bonds.

if i ignore the above things,go on the command ,when runing the em.mdp there is 
a tip that Steepest Descents failed converged to Fmax < 1000 in 5001 steps.when 
run the pr.tpr,a error emerged as segment fatal error。

2 someone told me that i need both suitable parameters for your desired force 
field, and then to construct a correct topology. I read lots of papers,but most 
of them used amber force field.Does anyone known a paper with a gromacs force 
field for HEME group?

please help me how handle those problems,how can i go on the simulation?

the HEME-cysteine parameter in the rtp files,define themas a new residue.(is 
there any problems?)

[ HEME ] 
 [ atoms ]   
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2-0.1 2
   SG S-0.4 2
C C 0.38000 3
O O-0.38000 3
   FEFE 0.84700 4
   NANR-0.37000 4
   NBNR-0.42300 4
   NCNR-0.50400 4

 [ bonds ]   
N Hgb_2  
NCAgb_20 
   CA Cgb_26 
C Ogb_4  
C+Ngb_9  
   CACBgb_26 
   CBSGgb_30 
   SGFEgb_48 
   FENAgb_34 
   FENBgb_34 
   FENCgb_34 
   FENDgb_34   

.  
 [ angles ]  
;  aiajak   gromos type  
   -C N H ga_31  
H NCA ga_17  
   -C NCA ga_30  
NCA C ga_12  
   CA C+N ga_18  
   CA C O ga_29  
 ...   
 [ impropers ]   
;  aiajakal   gromos type
N-CCA H gi_1 
CCA+N O gi_1 
   CA N CCB gi_2 
   FESGNAND gi_3 
   FESGNANB gi_3 
   FESGNBNC gi_3 
   FESGNCND gi_3 
  . 
 [ dihedrals ]   
;  aiajakal   gromos type
  .


没有广告的终身免费邮箱,www.yeah.net





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Re: [gmx-users] error while executing grompp

[Justin A. Lemkul]

Chanchal wrote:

Hi Justin,
 I have corrected the ffcharmm.itp file. But I am still getting the 
error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#

checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations

---
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273

Fatal error:
[ file topol.top, line 3879 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---



Well, then I'm out of ideas.  Your files work for me; I can successfully produce 
a .tpr file using a basic EM .mdp file.  Have you validated your installation 
using the test set?  Have you made any modifications to the standard tip3p.itp file?


-Justin


Thanks
Chanchal


On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul > wrote:




Chanchal wrote:

Hi Justin,
 Sorry, I attached the wrong file. Attached is the correct file.


There is a space after #define:

#define _FF_CHARMM

Your file has #define_FF_CHARMM.

-Justin

Thanks
Chanchal



On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Chanchal wrote:

   Hi Justin,
I am still getting the error message : Back Off! I just
backed
   up mdout.mdp to ./#mdout.mdp.2#
   checking input for internal consistency...
   processing topology...
   Generated 0 of the 595 non-bonded parameter combinations

   ---
   Program grompp_d, VERSION 4.0.5
   Source code file: toppush.c, line: 1273

   Fatal error:
   [ file topol.top, line 3879 ]:
   Atom index (1) in settles out of bounds (1-0).
   This probably means that you have inserted topology section
   "settles"
   in a part belonging to a different molecule than you
intended to.
   In that case move the "settles" section to the right
molecule.
   ---

   As you said I added the line #define_FF_CHARMM in
ffcharmm.itp.
   Attached


   The #define line is not present in that file.  Take care to
use the
   right files when you've made changes.

   -Justin

   is the file.
   Thanks
   Chanchal


   On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

>
   
>>
  
>
   
 wrote:



 Chanchal wrote:

 Hi All,
   I have downloaded pdb file and required
.top and
   .itp file
 from the site
http://www.bioinf.uni-sb.de/RB/ for DOPC
 simulation. Now when I execute the command
  grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p
   topol.top -o
 dopc.tpr -e ener.edr -t traj.trr I got the
error "
   Fatal
  error:
   

Re: [gmx-users] genion question

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:



You chose the wrong terminus.  The Zwitterion-NH3+ species is for an isolated 
amino acid containing both NH3+ and COO- alpha-carbon substituents.  Choose a 
plain NH3+ for your terminus.


-Justin


 1   opls_287  1ASP  N  1   -0.314.0067   ; qtot
-0.3
 2   opls_290  1ASP H1  1   0.33  1.008   ;
qtot 0.03
 3   opls_290  1ASP H2  1   0.33  1.008   ;
qtot 0.36
 4   opls_290  1ASP H3  1   0.33  1.008   ;
qtot 0.69
 5   opls_299  1ASP CA  1   0.15 12.011   ;
qtot 0.84
 6   opls_140  1ASP HA  1   0.06  1.008   ;
qtot 0.9
 7   opls_274  1ASP CB  2  -0.22 12.011   ;
qtot 0.68
 8   opls_140  1ASPHB1  2   0.06  1.008   ;
qtot 0.74
 9   opls_140  1ASPHB2  2   0.06  1.008   ;
qtot 0.8
10   opls_271  1ASP CG  30.7 12.011   ;
qtot 1.5
11   opls_272  1ASPOD1  3   -0.815.9994   ;
qtot 0.7
12   opls_272  1ASPOD2  3   -0.815.9994   ;
qtot -0.1
13   opls_235  1ASP  C  40.5 12.011   ;
qtot 0.4
14   opls_236  1ASP  O  4   -0.515.9994   ;
qtot -0.1

What do you think?

Payman





On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!

The total charge will undoubtedly fluctuate.  What's most important to look at 
is when you reach the end of a residue and you do not see an integer charge.


-Justin


Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the

No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:

[ moleculetype ]
; molname   nrexcl
NA+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_4071   NA+ NA   1  1   22.98977


-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:

  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!

I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
to see where things start going wrong (i.e., not an integer).  I would think 
your system would have to be quite large to accumulate such a difference in charge.


-Justin


Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
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Re: [gmx-users] genion question

[Paymon Pirzadeh]

Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:

 1   opls_287  1ASP  N  1   -0.314.0067   ; qtot
-0.3
 2   opls_290  1ASP H1  1   0.33  1.008   ;
qtot 0.03
 3   opls_290  1ASP H2  1   0.33  1.008   ;
qtot 0.36
 4   opls_290  1ASP H3  1   0.33  1.008   ;
qtot 0.69
 5   opls_299  1ASP CA  1   0.15 12.011   ;
qtot 0.84
 6   opls_140  1ASP HA  1   0.06  1.008   ;
qtot 0.9
 7   opls_274  1ASP CB  2  -0.22 12.011   ;
qtot 0.68
 8   opls_140  1ASPHB1  2   0.06  1.008   ;
qtot 0.74
 9   opls_140  1ASPHB2  2   0.06  1.008   ;
qtot 0.8
10   opls_271  1ASP CG  30.7 12.011   ;
qtot 1.5
11   opls_272  1ASPOD1  3   -0.815.9994   ;
qtot 0.7
12   opls_272  1ASPOD2  3   -0.815.9994   ;
qtot -0.1
13   opls_235  1ASP  C  40.5 12.011   ;
qtot 0.4
14   opls_236  1ASP  O  4   -0.515.9994   ;
qtot -0.1

What do you think?

Payman





On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Well, when I look into my .top file, almost no where I see closeness to
> > an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
> > sometimes. But I can not see a clear trend on where things go wrong. My
> > protein has only 37 amino acids with 451 atoms (including hydrogens).
> > I am not sure if I can attach the .top file to my e-mail for you to
> > check. This way I could learn where and how things go wrong!
> > 
> 
> The total charge will undoubtedly fluctuate.  What's most important to look 
> at 
> is when you reach the end of a residue and you do not see an integer charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Thanks for the tips!
> >>> But I still have problem with my added ion. Justin had told me that ion
> >>> names are force-field specific! Since I am using OPLSaa, I checked the
> >>> itp file for Na ion name, and it was Na+. I used this name with the
> >> No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:
> >>
> >> [ moleculetype ]
> >> ; molname   nrexcl
> >> NA+ 1
> >>
> >> [ atoms ]
> >> ; idat type res nr  residu name at name  cg nr  charge   
> >> mass
> >> 1   opls_4071   NA+ NA   1  1   
> >> 22.98977
> >>
> >>> -pname switch, but again during the grompp I ran into the following
> >>> error:
> >>> Warning: atom name 65870 in AFP_I.top and
> >>> AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
> >>>
> >>> WARNING 1 [file AFP_I.top, line 4151]:
> >>>   1 non-matching atom name
> >>>   atom names from AFP_I.top will be used
> >>>   atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
> >>>
> >>> I really do not know what I am doing wrong here! Also regarding past
> >>> discussions, adding this single ion has lead into the following note:
> >>>  
> >>> NOTE 1 [file AFP_I.top, line 4151]:
> >>>   System has non-zero total charge: 1.00e-02
> >>>
> >>> I am not sure if that much charge will cause me troubles or not!
> >>>
> >> I am somewhat troubled by the magnitude of charge discrepancy.  Look in 
> >> the .top 
> >> to see where things start going wrong (i.e., not an integer).  I would 
> >> think 
> >> your system would have to be quite large to accumulate such a difference 
> >> in charge.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
>  Paymon Pirzadeh wrote:
> > Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> > negative charge exactly? Does that hurt science or simulation?
>  It's probably irrelevant. The representation of "decimal" numbers on 
>  computers can be inexact, such that things like 0.02 added to itself 100 
>  times does not pass a test for equality with 2. You may be observing 
>  this kind of thing here. Your protein's [atoms] directive has a running 
>  count of the total  charge on the molecule - go and read it and see that 
>  each residue has an integral charge. Hopefully you can observe where the 
>  rounding error might be occurring and you can make a judgement about 
>  whether this might be true.
> 
>  Mark
>  ___
>  gmx-users mailing listgmx-users@gromacs.org
>  http://lists.gromacs.org/m

Re: [gmx-users] error while executing grompp

[Chanchal]

Hi Justin,
 I have corrected the ffcharmm.itp file. But I am still getting the error:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations

---
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273

Fatal error:
[ file topol.top, line 3879 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

Thanks
Chanchal


On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul  wrote:

>
>
> Chanchal wrote:
>
>> Hi Justin,
>>  Sorry, I attached the wrong file. Attached is the correct file.
>>
>
> There is a space after #define:
>
> #define _FF_CHARMM
>
> Your file has #define_FF_CHARMM.
>
> -Justin
>
>  Thanks
>> Chanchal
>>
>>
>> On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Chanchal wrote:
>>
>>Hi Justin,
>> I am still getting the error message : Back Off! I just backed
>>up mdout.mdp to ./#mdout.mdp.2#
>>checking input for internal consistency...
>>processing topology...
>>Generated 0 of the 595 non-bonded parameter combinations
>>
>>---
>>Program grompp_d, VERSION 4.0.5
>>Source code file: toppush.c, line: 1273
>>
>>Fatal error:
>>[ file topol.top, line 3879 ]:
>>Atom index (1) in settles out of bounds (1-0).
>>This probably means that you have inserted topology section
>>"settles"
>>in a part belonging to a different molecule than you intended to.
>>In that case move the "settles" section to the right molecule.
>>---
>>
>>As you said I added the line #define_FF_CHARMM in ffcharmm.itp.
>>Attached
>>
>>
>>The #define line is not present in that file.  Take care to use the
>>right files when you've made changes.
>>
>>-Justin
>>
>>is the file.
>>Thanks
>>Chanchal
>>
>>
>>On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>   Your ffcharmm.itp file lacks a necessary line at the very top:
>>
>>   #define _FF_CHARMM
>>
>>   Without this line, grompp does not know which force field you
>> are
>>   using, and hence everything breaks down when other .itp files
>> are
>>   called.
>>
>>   -Justin
>>
>>   Chanchal wrote:
>>
>>   Hi,
>>Attached are the top and itp file I am using. Please
>>help me to
>>   fix the problem.
>>   Thanks
>>   Chanchal
>>
>>
>>   On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul
>>   mailto:jalem...@vt.edu>
>>>
>>   
>>>
>>
>>
>>  Chanchal wrote:
>>
>>  Hi All,
>>I have downloaded pdb file and required .top and
>>.itp file
>>  from the site http://www.bioinf.uni-sb.de/RB/ for
>> DOPC
>>  simulation. Now when I execute the command
>>   grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p
>>topol.top -o
>>  dopc.tpr -e ener.edr -t traj.trr I got the error "
>>Fatal
>>   error:
>>  [ file tip3p.itp, line 42 ]:
>>  Atom index (1) in settles out of bounds (1-0).
>>  This probably means that you have inserted
>>topology section
>>  "settles"
>>  in a part belonging to a different molecule than you
>>   intended to.
>>  In that case move the "settles" section to the right
>>   molecule.
>>
>>  ---
>>
>>  Attached is the em.mdp file I am using. Please
>>help me how to
>>  solve this problem.
>>
>>
>>  Please see here:
>>
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds
>>
>>  The .mdp file is not the source of the problem; the
>>topology
>>   is.  If
>>  you need more help, you'll have to post the relevant
>>section.
>>
>>  -Justin
>>
>>   

Re: [gmx-users] error while executing grompp

[Justin A. Lemkul]

Chanchal wrote:

Hi Justin,
  Sorry, I attached the wrong file. Attached is the correct file.


There is a space after #define:

#define _FF_CHARMM

Your file has #define_FF_CHARMM.

-Justin


Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul > wrote:




Chanchal wrote:

Hi Justin,
 I am still getting the error message : Back Off! I just backed
up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations

---
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273

Fatal error:
[ file topol.top, line 3879 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section
"settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

As you said I added the line #define_FF_CHARMM in ffcharmm.itp.
Attached


The #define line is not present in that file.  Take care to use the
right files when you've made changes.

-Justin

is the file.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   Your ffcharmm.itp file lacks a necessary line at the very top:

   #define _FF_CHARMM

   Without this line, grompp does not know which force field you are
   using, and hence everything breaks down when other .itp files are
   called.

   -Justin

   Chanchal wrote:

   Hi,
Attached are the top and itp file I am using. Please
help me to
   fix the problem.
   Thanks
   Chanchal


   On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

   >
   >>


  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
http://www.gromacs.org/search
  before posting!
  Please don't post (un)subscribe requests to the
list. Use the
  www interface or send it to
gmx-users-requ...@gromacs.org 
   

Re: [gmx-users] error while executing grompp

[Chanchal]

Hi Justin,
  Sorry, I attached the wrong file. Attached is the correct file.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul  wrote:

>
>
> Chanchal wrote:
>
>> Hi Justin,
>>  I am still getting the error message : Back Off! I just backed up
>> mdout.mdp to ./#mdout.mdp.2#
>> checking input for internal consistency...
>> processing topology...
>> Generated 0 of the 595 non-bonded parameter combinations
>>
>> ---
>> Program grompp_d, VERSION 4.0.5
>> Source code file: toppush.c, line: 1273
>>
>> Fatal error:
>> [ file topol.top, line 3879 ]:
>> Atom index (1) in settles out of bounds (1-0).
>> This probably means that you have inserted topology section "settles"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "settles" section to the right molecule.
>> ---
>>
>> As you said I added the line #define_FF_CHARMM in ffcharmm.itp. Attached
>>
>
> The #define line is not present in that file.  Take care to use the right
> files when you've made changes.
>
> -Justin
>
>  is the file.
>> Thanks
>> Chanchal
>>
>>
>> On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>Your ffcharmm.itp file lacks a necessary line at the very top:
>>
>>#define _FF_CHARMM
>>
>>Without this line, grompp does not know which force field you are
>>using, and hence everything breaks down when other .itp files are
>>called.
>>
>>-Justin
>>
>>Chanchal wrote:
>>
>>Hi,
>> Attached are the top and itp file I am using. Please help me to
>>fix the problem.
>>Thanks
>>Chanchal
>>
>>
>>On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Chanchal wrote:
>>
>>   Hi All,
>> I have downloaded pdb file and required .top and .itp file
>>   from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
>>   simulation. Now when I execute the command
>>grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
>>   dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal
>>error:
>>   [ file tip3p.itp, line 42 ]:
>>   Atom index (1) in settles out of bounds (1-0).
>>   This probably means that you have inserted topology section
>>   "settles"
>>   in a part belonging to a different molecule than you
>>intended to.
>>   In that case move the "settles" section to the right
>>molecule.
>>   ---
>>
>>   Attached is the em.mdp file I am using. Please help me how
>> to
>>   solve this problem.
>>
>>
>>   Please see here:
>>
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds
>>
>>   The .mdp file is not the source of the problem; the topology
>>is.  If
>>   you need more help, you'll have to post the relevant section.
>>
>>   -Justin
>>
>>   Thanks
>>   Chanchal
>>
>>
>>
>> 
>>
>>   ___
>>   gmx-users mailing listgmx-users@gromacs.org
>>
>>   > >>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at http://www.gromacs.org/search
>>   before posting!
>>   Please don't post (un)subscribe requests to the list. Use
>> the
>>   www interface or send it to gmx-users-requ...@gromacs.org
>>
>>   >>.
>>
>>   Can't post? Read
>>http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>   --
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>231-9080
>>
>>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>   
>>   ___
>>   gmx-users mailing listgmx-users@gromacs.org
>>
>>   >
>>
>>
>>   http://lists.gromacs.o

Re: [gmx-users] error while executing grompp

[Justin A. Lemkul]

Chanchal wrote:

Hi Justin,
  I am still getting the error message : Back Off! I just backed up 
mdout.mdp to ./#mdout.mdp.2#

checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations

---
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273

Fatal error:
[ file topol.top, line 3879 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

As you said I added the line #define_FF_CHARMM in ffcharmm.itp. Attached 


The #define line is not present in that file.  Take care to use the right files 
when you've made changes.


-Justin


is the file.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul > wrote:



Your ffcharmm.itp file lacks a necessary line at the very top:

#define _FF_CHARMM

Without this line, grompp does not know which force field you are
using, and hence everything breaks down when other .itp files are
called.

-Justin

Chanchal wrote:

Hi,
 Attached are the top and itp file I am using. Please help me to
fix the problem.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Chanchal wrote:

   Hi All,
 I have downloaded pdb file and required .top and .itp file
   from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
   simulation. Now when I execute the command
grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
   dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal
error:
   [ file tip3p.itp, line 42 ]:
   Atom index (1) in settles out of bounds (1-0).
   This probably means that you have inserted topology section
   "settles"
   in a part belonging to a different molecule than you
intended to.
   In that case move the "settles" section to the right
molecule.
   ---

   Attached is the em.mdp file I am using. Please help me how to
   solve this problem.


   Please see here:

 
 http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds


   The .mdp file is not the source of the problem; the topology
is.  If
   you need more help, you'll have to post the relevant section.

   -Justin

   Thanks
   Chanchal


 
 


   ___
   gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search
   before posting!
   Please don't post (un)subscribe requests to the list. Use the
   www interface or send it to gmx-users-requ...@gromacs.org

   >.

   Can't post? Read
http://www.gromacs.org/mailing_lists/users.php


   --

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   
   ___
   gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search before
   posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.

Re: [gmx-users] error while executing grompp

[Chanchal]

Hi Justin,
  I am still getting the error message : Back Off! I just backed up
mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations

---
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273

Fatal error:
[ file topol.top, line 3879 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

As you said I added the line #define_FF_CHARMM in ffcharmm.itp. Attached is
the file.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul  wrote:

>
> Your ffcharmm.itp file lacks a necessary line at the very top:
>
> #define _FF_CHARMM
>
> Without this line, grompp does not know which force field you are using,
> and hence everything breaks down when other .itp files are called.
>
> -Justin
>
> Chanchal wrote:
>
>> Hi,
>>  Attached are the top and itp file I am using. Please help me to fix the
>> problem.
>> Thanks
>> Chanchal
>>
>>
>> On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Chanchal wrote:
>>
>>Hi All,
>>  I have downloaded pdb file and required .top and .itp file
>>from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
>>simulation. Now when I execute the command
>> grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
>>dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal error:
>>[ file tip3p.itp, line 42 ]:
>>Atom index (1) in settles out of bounds (1-0).
>>This probably means that you have inserted topology section
>>"settles"
>>in a part belonging to a different molecule than you intended to.
>>In that case move the "settles" section to the right molecule.
>>---
>>
>>Attached is the em.mdp file I am using. Please help me how to
>>solve this problem.
>>
>>
>>Please see here:
>>
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds
>>
>>The .mdp file is not the source of the problem; the topology is.  If
>>you need more help, you'll have to post the relevant section.
>>
>>-Justin
>>
>>Thanks
>>Chanchal
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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ffcharmm.itp
Description: Binary data
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Re: [gmx-users] genion question

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!



The total charge will undoubtedly fluctuate.  What's most important to look at 
is when you reach the end of a residue and you do not see an integer charge.


-Justin


Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the

No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:

[ moleculetype ]
; molname   nrexcl
NA+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_4071   NA+ NA   1  1   22.98977


-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:

  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!

I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
to see where things start going wrong (i.e., not an integer).  I would think 
your system would have to be quite large to accumulate such a difference in charge.


-Justin


Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] make_ndx help

[Justin A. Lemkul]

parthi...@ncbs.res.in wrote:

Hi

Anyone can please tell how to index 2 or more groups using make_ndx

eg: 1 protein
12 sol
13 NA+
i tried giving >1&12, which shows that the "Group is empty"


Type "help" at the make_ndx prompt; you will see a number of examples.

There are also more examples on the wiki:

http://oldwiki.gromacs.org/index.php/make_ndx

-Justin



thanks in advance
Parthiban

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] make_ndx help

[TJ Piggot]

1|12 merges the two groups into a new group

(1&12 will merge into a new group any atoms which are in both groups 1 and 
12, of which there are none in this case)


Tom

--On Wednesday, August 26, 2009 04:07:20 +0530 parthi...@ncbs.res.in wrote:


Hi

Anyone can please tell how to index 2 or more groups using make_ndx

eg: 1 protein
12 sol
13 NA+
i tried giving >1&12, which shows that the "Group is empty"

thanks in advance
Parthiban

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--
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.

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[gmx-users] make_ndx help

[parthiban]

Hi

Anyone can please tell how to index 2 or more groups using make_ndx

eg: 1 protein
12 sol
13 NA+
i tried giving >1&12, which shows that the "Group is empty"

thanks in advance
Parthiban

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Re: [gmx-users] error while executing grompp

[Justin A. Lemkul]

Your ffcharmm.itp file lacks a necessary line at the very top:

#define _FF_CHARMM

Without this line, grompp does not know which force field you are using, and 
hence everything breaks down when other .itp files are called.


-Justin

Chanchal wrote:

Hi,
  Attached are the top and itp file I am using. Please help me to fix 
the problem.

Thanks
Chanchal


On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul > wrote:




Chanchal wrote:

Hi All,
  I have downloaded pdb file and required .top and .itp file
from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
simulation. Now when I execute the command
 grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal error:
[ file tip3p.itp, line 42 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section
"settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

Attached is the em.mdp file I am using. Please help me how to
solve this problem.


Please see here:


http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds

The .mdp file is not the source of the problem; the topology is.  If
you need more help, you'll have to post the relevant section.

-Justin

Thanks
Chanchal




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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] genion question

[Paymon Pirzadeh]

Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!

Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Thanks for the tips!
> > But I still have problem with my added ion. Justin had told me that ion
> > names are force-field specific! Since I am using OPLSaa, I checked the
> > itp file for Na ion name, and it was Na+. I used this name with the
> 
> No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:
> 
> [ moleculetype ]
> ; molname   nrexcl
> NA+ 1
> 
> [ atoms ]
> ; idat type res nr  residu name at name  cg nr  charge   mass
> 1   opls_4071   NA+ NA   1  1   
> 22.98977
> 
> > -pname switch, but again during the grompp I ran into the following
> > error:
> > Warning: atom name 65870 in AFP_I.top and
> > AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
> > 
> > WARNING 1 [file AFP_I.top, line 4151]:
> >   1 non-matching atom name
> >   atom names from AFP_I.top will be used
> >   atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
> > 
> > I really do not know what I am doing wrong here! Also regarding past
> > discussions, adding this single ion has lead into the following note:
> >  
> > NOTE 1 [file AFP_I.top, line 4151]:
> >   System has non-zero total charge: 1.00e-02
> > 
> > I am not sure if that much charge will cause me troubles or not!
> > 
> 
> I am somewhat troubled by the magnitude of charge discrepancy.  Look in the 
> .top 
> to see where things start going wrong (i.e., not an integer).  I would think 
> your system would have to be quite large to accumulate such a difference in 
> charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> >> Paymon Pirzadeh wrote:
> >>> Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> >>> negative charge exactly? Does that hurt science or simulation?
> >> It's probably irrelevant. The representation of "decimal" numbers on 
> >> computers can be inexact, such that things like 0.02 added to itself 100 
> >> times does not pass a test for equality with 2. You may be observing 
> >> this kind of thing here. Your protein's [atoms] directive has a running 
> >> count of the total  charge on the molecule - go and read it and see that 
> >> each residue has an integral charge. Hopefully you can observe where the 
> >> rounding error might be occurring and you can make a judgement about 
> >> whether this might be true.
> >>
> >> Mark
> >> ___
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
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> >>
> >>
> > 
> > ___
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
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> > 
> 

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Re: [gmx-users] genion question

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the


No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:

[ moleculetype ]
; molname   nrexcl
NA+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_4071   NA+ NA   1  1   22.98977


-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:

  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!



I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
to see where things start going wrong (i.e., not an integer).  I would think 
your system would have to be quite large to accumulate such a difference in charge.


-Justin


Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] genion question

[Paymon Pirzadeh]

Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the
-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
 
NOTE 1 [file AFP_I.top, line 4151]:
  System has non-zero total charge: 1.00e-02

I am not sure if that much charge will cause me troubles or not!

Payman





On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> Paymon Pirzadeh wrote:
> > Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> > negative charge exactly? Does that hurt science or simulation?
> 
> It's probably irrelevant. The representation of "decimal" numbers on 
> computers can be inexact, such that things like 0.02 added to itself 100 
> times does not pass a test for equality with 2. You may be observing 
> this kind of thing here. Your protein's [atoms] directive has a running 
> count of the total  charge on the molecule - go and read it and see that 
> each residue has an integral charge. Hopefully you can observe where the 
> rounding error might be occurring and you can make a judgement about 
> whether this might be true.
> 
> Mark
> ___
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> 
> 

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Re: [gmx-users] Mdrun error

[Mark Abraham]

Cíntia C. Vequi-Suplicy wrote:

Hello Justin,

I used Gromacs 4.0.5 and the error was gone. Thank you.

But now I have another problem when using mdrun_d. I gave the comand:

mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &

And first I got  a lot of output on the shell window and I think it is 
strange. This output should be on a file or not?


No, this output to stdout is normal. 3.3.3 does that too. Roughly the 
same content got written to the .log file. It sounds like you should do 
some tutorial material to get used to the GROMACS workflow.



And  after a few seconds I got an error which says:

t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#

Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
Wrote pdb files with previous and current coordinates
MPI process rank 0 (n0, p23764) caught a SIGSEGV.


See 
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings


You should do some searching on the wiki/web to help diagnose your own 
problems before asking here :-) You'll learn more about problems you've 
solved yourself :-)


Mark
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[gmx-users] Re: Mdrun error

[Justin A. Lemkul]

Cíntia C. Vequi-Suplicy wrote:

Hello Justin,

I used Gromacs 4.0.5 and the error was gone. Thank you.

But now I have another problem when using mdrun_d. I gave the comand:

mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &

And first I got  a lot of output on the shell window and I think it is 
strange. This output should be on a file or not?

And  after a few seconds I got an error which says:

t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#

Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
Wrote pdb files with previous and current coordinates
MPI process rank 0 (n0, p23764) caught a SIGSEGV.

Can you help me?



Your system is unstable and thus blowing up, due to any number of factors 
including incorrect force field parameters, inappropriate .mdp settings, 
insufficient minimization and/or equilibration, or any combination of the above.


Advice from the wiki:

http://oldwiki.gromacs.org/index.php/blowing_up

-Justin


Thank you
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University

Justin A. Lemkul wrote:



Cíntia C. Vequi-Suplicy wrote:

Hello,

I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dppc128.top > gromppzJXISa'cpp
' command is defined in the .mdp file
*
* Important: if you do not have a c-preprocessor installed, *
* you MUST run grompp with the "-pp" command line option*
* in place of the "-p" option.  *
*
processing topology...
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (dppc128.gro, 17365)
   does not match topology (dppc128.top, 0)
---

"One Cross Each" (Monty Python)

I don´t where the problem is, I've already checked the cpp compiler and
it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
topology file I have the following lines:



Have you tried the advice from grompp to use -pp instead of -p?

General advice for this problem can be found here:

http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology 



Also an option is to upgrade to the most recent version of Gromacs 
(4.0.5), which does not require cpp.


-Justin


;
;File 'dppc128.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Aug 18 10:02:52 2009
;
;This is your topology file
;Pure DPPC bilayer with 128 lipids and 3655 water molecules
;
; The force field files to be include
#include "ffoplsaa.itp"
; Include DPPC topology
#include "dppc.itp"
#include "lipid.itp"
#include "spc.itp"

[ molecules ]
; Compound   #mol
DPP  128
SOL  3655

If anyone can help It will be very nice,

Thank you very much so far,
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] genion question

[Mark Abraham]

Paymon Pirzadeh wrote:

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?


It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


Mark
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[gmx-users] Mdrun error

Hello Justin,

I used Gromacs 4.0.5 and the error was gone. Thank you.

But now I have another problem when using mdrun_d. I gave the comand:

mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &

And first I got  a lot of output on the shell window and I think it is 
strange. This output should be on a file or not?

And  after a few seconds I got an error which says:

t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#

Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
Wrote pdb files with previous and current coordinates
MPI process rank 0 (n0, p23764) caught a SIGSEGV.

Can you help me?

Thank you
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University

Justin A. Lemkul wrote:



Cíntia C. Vequi-Suplicy wrote:

Hello,

I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dppc128.top > gromppzJXISa'cpp
' command is defined in the .mdp file
*
* Important: if you do not have a c-preprocessor installed, *
* you MUST run grompp with the "-pp" command line option*
* in place of the "-p" option.  *
*
processing topology...
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (dppc128.gro, 17365)
   does not match topology (dppc128.top, 0)
---

"One Cross Each" (Monty Python)

I don´t where the problem is, I've already checked the cpp compiler and
it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
topology file I have the following lines:



Have you tried the advice from grompp to use -pp instead of -p?

General advice for this problem can be found here:

http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology 



Also an option is to upgrade to the most recent version of Gromacs 
(4.0.5), which does not require cpp.


-Justin


;
;File 'dppc128.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Aug 18 10:02:52 2009
;
;This is your topology file
;Pure DPPC bilayer with 128 lipids and 3655 water molecules
;
; The force field files to be include
#include "ffoplsaa.itp"
; Include DPPC topology
#include "dppc.itp"
#include "lipid.itp"
#include "spc.itp"

[ molecules ]
; Compound   #mol
DPP  128
SOL  3655

If anyone can help It will be very nice,

Thank you very much so far,
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University
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Re: [gmx-users] error while executing grompp

[Mark Abraham]

Chanchal wrote:

Hi All,
   I have downloaded pdb file and required .top and .itp file from the site
http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I execute the
command
 grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e
ener.edr -t traj.trr I got the error " Fatal error:
[ file tip3p.itp, line 42 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

Attached is the em.mdp file I am using. Please help me how to solve this
problem.


Your .mdp file isn't the problem. grompp is telling you what the problem 
is likely to be. The .top/.itp combination you are using is broken. See 
also 
http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds


Mark
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Re: [gmx-users] genion question

[Paymon Pirzadeh]

Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?

Payman 


On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > I realized sth about the previous error message I posted. In the
> > following I have copied the lines (with their line number) which
> > grompp gives warning on! 
> > 
> > 
> > in .gro file:
> > 65868 10940SOLHW265866   5.038   5.739   6.407
> > 65869 10940SOL MW65867   5.103   5.710   6.455
> > 65870 10940SOLLP165868   5.061   5.644   6.524
> > 65871 10940SOLLP265869   5.144   5.630   6.405
> > 65872 10941Na  Na65870   1.844   0.957   1.889
> > 658735.4   6.23500  10.24600
> > 
> > in .top file:
> > 4147 [ molecules ]
> > 4148 ; Compound#mols
> > 4149 Protein_A   1
> > 4150 SOL 10903
> > 4151 Na+  1
> > 
> > I have tested that if I remove the "+" sign, grompp will not work at all
> > and says "such molecule does not exists". 
> > So, I am not sure where the Na-NA mismatch comes from?!
> > 
> 
> Ion names are force field-specific.  If you left -pname as the default, it 
> assigns Na (for ffgmx).  Check ions.itp for the correct name.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> When I look at the .top file generated by pdb2gmx, the last lines show
> >>> how this -0.99 is generated:
> >>>
> >>>442   opls_302 37ARG CZ138   0.64 12.011   ;
> >>> qtot -0.33
> >>>443   opls_300 37ARGNH1139   -0.814.0067   ;
> >>> qtot -1.13
> >>>444   opls_301 37ARG   HH11139   0.46  1.008   ;
> >>> qtot -0.67
> >>>445   opls_301 37ARG   HH12139   0.46  1.008   ;
> >>> qtot -0.21
> >>>446   opls_300 37ARGNH2140   -0.814.0067   ;
> >>> qtot -1.01
> >>>447   opls_301 37ARG   HH21140   0.46  1.008   ;
> >>> qtot -0.55
> >>>448   opls_301 37ARG   HH22140   0.46  1.008   ;
> >>> qtot -0.09
> >>>449   opls_271 37ARG  C1410.7 12.011   ;
> >>> qtot 0.61
> >>>450   opls_272 37ARG O1141   -0.815.9994   ;
> >>> qtot -0.19
> >>>451   opls_272 37ARG O2141   -0.815.9994   ;
> >>> qtot -0.99
> >>>
> >>> The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
> >>> simulation is supposed to be close to 7.0, I believe one of the
> >>> negatively-charged side chains needs to be neutralized. That's why I
> >>> think one Na+ might be helpful.
> >>>
> >> That's probably correct.  I just wanted to verify what was in your system. 
> >>  If 
> >> you just had water, it made no sense.  But with a protein involved with 
> >> lots of 
> >> partial charges, these rounding issues do occur.  You really do have a 
> >> system 
> >> with -1 charge.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > OK! It worked! Thanks a lot again. But I have a final technical
> > question. After running grompp, it shows that my box has a net charge of
> > -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> > OK?! or even this 0.01 charge will cause me troubles?
>  Depending on the size of your system, rounding errors can occur.  It is 
>  unusual 
>  that the hundredths place would be showing this error.  Usually you'd 
>  get 
>  something like 0.8 or something.  Your water topology has a zero net 
>  charge; 
>  is there something else in your system causing the -1 charge?
> 
>  Adding a single Na+ to neutralize the charge may be appropriate, but 
>  that's up 
>  to you based on what's in your system (something else may be broken, but 
>  I just 
>  don't know).
> 
>  -Justin
> 
> > Sorry for tons of e-mails.
> > regards,
> >
> > Payman
> >
> >
> > On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! That's fine. But what if I do not have permissions to make such
> >>> changes in the itp files? Also, isn't that the case that when you 
> >>> define
> >> That's why I said copy the force field files into your local 
> >> directory.  Once 
> >> there, you can modify them.
> >>
> >>> sth for the second time, grompp will take the second one? Sorry for 
> >>> mass
> >>> of e-mail!
> >>>
> >> That is only true in the case of .mdp files.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > I have done that already! I use my local copy

Re: [gmx-users] error while executing grompp

[Justin A. Lemkul]

Chanchal wrote:

Hi All,
   I have downloaded pdb file and required .top and .itp file from the 
site http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I 
execute the command
 grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e 
ener.edr -t traj.trr I got the error " Fatal error:

[ file tip3p.itp, line 42 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

Attached is the em.mdp file I am using. Please help me how to solve this 
problem.




Please see here:

http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds

The .mdp file is not the source of the problem; the topology is.  If you need 
more help, you'll have to post the relevant section.


-Justin


Thanks
Chanchal




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] error while executing grompp

[Chanchal]

Hi All,
   I have downloaded pdb file and required .top and .itp file from the site
http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I execute the
command
 grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e
ener.edr -t traj.trr I got the error " Fatal error:
[ file tip3p.itp, line 42 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
---

Attached is the em.mdp file I am using. Please help me how to solve this
problem.

Thanks
Chanchal


em.mdp
Description: Binary data
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Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

I realized sth about the previous error message I posted. In the
following I have copied the lines (with their line number) which
grompp gives warning on! 



in .gro file:
65868 10940SOLHW265866   5.038   5.739   6.407
65869 10940SOL MW65867   5.103   5.710   6.455
65870 10940SOLLP165868   5.061   5.644   6.524
65871 10940SOLLP265869   5.144   5.630   6.405
65872 10941Na  Na65870   1.844   0.957   1.889
658735.4   6.23500  10.24600

in .top file:
4147 [ molecules ]
4148 ; Compound#mols
4149 Protein_A   1
4150 SOL 10903
4151 Na+  1

I have tested that if I remove the "+" sign, grompp will not work at all
and says "such molecule does not exists". 
So, I am not sure where the Na-NA mismatch comes from?!




Ion names are force field-specific.  If you left -pname as the default, it 
assigns Na (for ffgmx).  Check ions.itp for the correct name.


-Justin


Payman








On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

When I look at the .top file generated by pdb2gmx, the last lines show
how this -0.99 is generated:

   442   opls_302 37ARG CZ138   0.64 12.011   ;
qtot -0.33
   443   opls_300 37ARGNH1139   -0.814.0067   ;
qtot -1.13
   444   opls_301 37ARG   HH11139   0.46  1.008   ;
qtot -0.67
   445   opls_301 37ARG   HH12139   0.46  1.008   ;
qtot -0.21
   446   opls_300 37ARGNH2140   -0.814.0067   ;
qtot -1.01
   447   opls_301 37ARG   HH21140   0.46  1.008   ;
qtot -0.55
   448   opls_301 37ARG   HH22140   0.46  1.008   ;
qtot -0.09
   449   opls_271 37ARG  C1410.7 12.011   ;
qtot 0.61
   450   opls_272 37ARG O1141   -0.815.9994   ;
qtot -0.19
   451   opls_272 37ARG O2141   -0.815.9994   ;
qtot -0.99

The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
simulation is supposed to be close to 7.0, I believe one of the
negatively-charged side chains needs to be neutralized. That's why I
think one Na+ might be helpful.

That's probably correct.  I just wanted to verify what was in your system.  If 
you just had water, it made no sense.  But with a protein involved with lots of 
partial charges, these rounding issues do occur.  You really do have a system 
with -1 charge.


-Justin


Payman


On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK! It worked! Thanks a lot again. But I have a final technical
question. After running grompp, it shows that my box has a net charge of
-0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
OK?! or even this 0.01 charge will cause me troubles?
Depending on the size of your system, rounding errors can occur.  It is unusual 
that the hundredths place would be showing this error.  Usually you'd get 
something like 0.8 or something.  Your water topology has a zero net charge; 
is there something else in your system causing the -1 charge?


Adding a single Na+ to neutralize the charge may be appropriate, but that's up 
to you based on what's in your system (something else may be broken, but I just 
don't know).


-Justin


Sorry for tons of e-mails.
regards,

Payman


On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK! That's fine. But what if I do not have permissions to make such
changes in the itp files? Also, isn't that the case that when you define
That's why I said copy the force field files into your local directory.  Once 
there, you can modify them.



sth for the second time, grompp will take the second one? Sorry for mass
of e-mail!


That is only true in the case of .mdp files.

-Justin


Payman



On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?


I don't understand what you're saying you've already done.

The problem is this: when grompp attempts to assemble the .tpr file, it reads 
all of the information from the ffoplsaa*.itp files.  It finds the directives 
like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it finds a 
duplicate of these directives, it complains.  So when you #include your .itp 
file with new [atomtypes], it generates the error because it is a duplicate 
directive.  You have to include the new atom types in ffoplsaanb.itp in the 
[atomtypes] directive of this file.  The rest of the topology shouldn't cause a 
problem, just the [atomtypes] directive.


-Justin


Payman
  





On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK!
here is the .itp file which I generated. I might upload it because it
has passed the 

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

I realized sth about the previous error message I posted. In the
following I have copied the lines (with their line number) which
grompp gives warning on! 


in .gro file:
65868 10940SOLHW265866   5.038   5.739   6.407
65869 10940SOL MW65867   5.103   5.710   6.455
65870 10940SOLLP165868   5.061   5.644   6.524
65871 10940SOLLP265869   5.144   5.630   6.405
65872 10941Na  Na65870   1.844   0.957   1.889
658735.4   6.23500  10.24600

in .top file:
4147 [ molecules ]
4148 ; Compound#mols
4149 Protein_A   1
4150 SOL 10903
4151 Na+  1

I have tested that if I remove the "+" sign, grompp will not work at all
and says "such molecule does not exists". 
So, I am not sure where the Na-NA mismatch comes from?!

Payman








On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > When I look at the .top file generated by pdb2gmx, the last lines show
> > how this -0.99 is generated:
> > 
> >442   opls_302 37ARG CZ138   0.64 12.011   ;
> > qtot -0.33
> >443   opls_300 37ARGNH1139   -0.814.0067   ;
> > qtot -1.13
> >444   opls_301 37ARG   HH11139   0.46  1.008   ;
> > qtot -0.67
> >445   opls_301 37ARG   HH12139   0.46  1.008   ;
> > qtot -0.21
> >446   opls_300 37ARGNH2140   -0.814.0067   ;
> > qtot -1.01
> >447   opls_301 37ARG   HH21140   0.46  1.008   ;
> > qtot -0.55
> >448   opls_301 37ARG   HH22140   0.46  1.008   ;
> > qtot -0.09
> >449   opls_271 37ARG  C1410.7 12.011   ;
> > qtot 0.61
> >450   opls_272 37ARG O1141   -0.815.9994   ;
> > qtot -0.19
> >451   opls_272 37ARG O2141   -0.815.9994   ;
> > qtot -0.99
> > 
> > The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
> > simulation is supposed to be close to 7.0, I believe one of the
> > negatively-charged side chains needs to be neutralized. That's why I
> > think one Na+ might be helpful.
> > 
> 
> That's probably correct.  I just wanted to verify what was in your system.  
> If 
> you just had water, it made no sense.  But with a protein involved with lots 
> of 
> partial charges, these rounding issues do occur.  You really do have a system 
> with -1 charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! It worked! Thanks a lot again. But I have a final technical
> >>> question. After running grompp, it shows that my box has a net charge of
> >>> -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> >>> OK?! or even this 0.01 charge will cause me troubles?
> >> Depending on the size of your system, rounding errors can occur.  It is 
> >> unusual 
> >> that the hundredths place would be showing this error.  Usually you'd get 
> >> something like 0.8 or something.  Your water topology has a zero net 
> >> charge; 
> >> is there something else in your system causing the -1 charge?
> >>
> >> Adding a single Na+ to neutralize the charge may be appropriate, but 
> >> that's up 
> >> to you based on what's in your system (something else may be broken, but I 
> >> just 
> >> don't know).
> >>
> >> -Justin
> >>
> >>> Sorry for tons of e-mails.
> >>> regards,
> >>>
> >>> Payman
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > OK! That's fine. But what if I do not have permissions to make such
> > changes in the itp files? Also, isn't that the case that when you define
>  That's why I said copy the force field files into your local directory.  
>  Once 
>  there, you can modify them.
> 
> > sth for the second time, grompp will take the second one? Sorry for mass
> > of e-mail!
> >
>  That is only true in the case of .mdp files.
> 
>  -Justin
> 
> > Payman
> >
> >
> >
> > On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> I have done that already! I use my local copy to make my files. but 
> >>> how
> >>> can I get rid of this error? get into the oplsaanb.itp or include this
> >>> water model in the topology file before oplsaa.itp?
> >>>
> >> I don't understand what you're saying you've already done.
> >>
> >> The problem is this: when grompp attempts to assemble the .tpr file, 
> >> it reads 
> >> all of the information from the ffoplsaa*.itp files.  It finds the 
> >> directives 
> >> like [defaults], [atomtypes], etc in a pre-defined order.  If, later, 
> >> it finds a 
> >> duplicate of these directives, it complains.  So when you #include 
> >> your .itp 
> >> file with new [atomtypes], it generates the error because it is a 
> 

[gmx-users] grompp warning with ion's name

[Paymon Pirzadeh]

After adding the Na ion, grompp gives the following error:


processing coordinates...
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)

WARNING 1 [file AFP_I.top, line 4151]:
  1 non-matching atom name
  atom names from AFP_I.top will be used
  atom names from AFP_I_solvated_54_62_102_null.gro will be ignored

This is while I could not find such the mentioned mismatch in the two
files. Should I ignore this warning? 

Payman





On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > When I look at the .top file generated by pdb2gmx, the last lines show
> > how this -0.99 is generated:
> > 
> >442   opls_302 37ARG CZ138   0.64 12.011   ;
> > qtot -0.33
> >443   opls_300 37ARGNH1139   -0.814.0067   ;
> > qtot -1.13
> >444   opls_301 37ARG   HH11139   0.46  1.008   ;
> > qtot -0.67
> >445   opls_301 37ARG   HH12139   0.46  1.008   ;
> > qtot -0.21
> >446   opls_300 37ARGNH2140   -0.814.0067   ;
> > qtot -1.01
> >447   opls_301 37ARG   HH21140   0.46  1.008   ;
> > qtot -0.55
> >448   opls_301 37ARG   HH22140   0.46  1.008   ;
> > qtot -0.09
> >449   opls_271 37ARG  C1410.7 12.011   ;
> > qtot 0.61
> >450   opls_272 37ARG O1141   -0.815.9994   ;
> > qtot -0.19
> >451   opls_272 37ARG O2141   -0.815.9994   ;
> > qtot -0.99
> > 
> > The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
> > simulation is supposed to be close to 7.0, I believe one of the
> > negatively-charged side chains needs to be neutralized. That's why I
> > think one Na+ might be helpful.
> > 
> 
> That's probably correct.  I just wanted to verify what was in your system.  
> If 
> you just had water, it made no sense.  But with a protein involved with lots 
> of 
> partial charges, these rounding issues do occur.  You really do have a system 
> with -1 charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! It worked! Thanks a lot again. But I have a final technical
> >>> question. After running grompp, it shows that my box has a net charge of
> >>> -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> >>> OK?! or even this 0.01 charge will cause me troubles?
> >> Depending on the size of your system, rounding errors can occur.  It is 
> >> unusual 
> >> that the hundredths place would be showing this error.  Usually you'd get 
> >> something like 0.8 or something.  Your water topology has a zero net 
> >> charge; 
> >> is there something else in your system causing the -1 charge?
> >>
> >> Adding a single Na+ to neutralize the charge may be appropriate, but 
> >> that's up 
> >> to you based on what's in your system (something else may be broken, but I 
> >> just 
> >> don't know).
> >>
> >> -Justin
> >>
> >>> Sorry for tons of e-mails.
> >>> regards,
> >>>
> >>> Payman
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > OK! That's fine. But what if I do not have permissions to make such
> > changes in the itp files? Also, isn't that the case that when you define
>  That's why I said copy the force field files into your local directory.  
>  Once 
>  there, you can modify them.
> 
> > sth for the second time, grompp will take the second one? Sorry for mass
> > of e-mail!
> >
>  That is only true in the case of .mdp files.
> 
>  -Justin
> 
> > Payman
> >
> >
> >
> > On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> I have done that already! I use my local copy to make my files. but 
> >>> how
> >>> can I get rid of this error? get into the oplsaanb.itp or include this
> >>> water model in the topology file before oplsaa.itp?
> >>>
> >> I don't understand what you're saying you've already done.
> >>
> >> The problem is this: when grompp attempts to assemble the .tpr file, 
> >> it reads 
> >> all of the information from the ffoplsaa*.itp files.  It finds the 
> >> directives 
> >> like [defaults], [atomtypes], etc in a pre-defined order.  If, later, 
> >> it finds a 
> >> duplicate of these directives, it complains.  So when you #include 
> >> your .itp 
> >> file with new [atomtypes], it generates the error because it is a 
> >> duplicate 
> >> directive.  You have to include the new atom types in ffoplsaanb.itp 
> >> in the 
> >> [atomtypes] directive of this file.  The rest of the topology 
> >> shouldn't cause a 
> >> problem, just the [atomtypes] directive.
> >>
> >> -Justin
> >>
> >>>

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

When I look at the .top file generated by pdb2gmx, the last lines show
how this -0.99 is generated:

   442   opls_302 37ARG CZ138   0.64 12.011   ;
qtot -0.33
   443   opls_300 37ARGNH1139   -0.814.0067   ;
qtot -1.13
   444   opls_301 37ARG   HH11139   0.46  1.008   ;
qtot -0.67
   445   opls_301 37ARG   HH12139   0.46  1.008   ;
qtot -0.21
   446   opls_300 37ARGNH2140   -0.814.0067   ;
qtot -1.01
   447   opls_301 37ARG   HH21140   0.46  1.008   ;
qtot -0.55
   448   opls_301 37ARG   HH22140   0.46  1.008   ;
qtot -0.09
   449   opls_271 37ARG  C1410.7 12.011   ;
qtot 0.61
   450   opls_272 37ARG O1141   -0.815.9994   ;
qtot -0.19
   451   opls_272 37ARG O2141   -0.815.9994   ;
qtot -0.99

The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
simulation is supposed to be close to 7.0, I believe one of the
negatively-charged side chains needs to be neutralized. That's why I
think one Na+ might be helpful.



That's probably correct.  I just wanted to verify what was in your system.  If 
you just had water, it made no sense.  But with a protein involved with lots of 
partial charges, these rounding issues do occur.  You really do have a system 
with -1 charge.


-Justin


Payman


On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK! It worked! Thanks a lot again. But I have a final technical
question. After running grompp, it shows that my box has a net charge of
-0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
OK?! or even this 0.01 charge will cause me troubles?
Depending on the size of your system, rounding errors can occur.  It is unusual 
that the hundredths place would be showing this error.  Usually you'd get 
something like 0.8 or something.  Your water topology has a zero net charge; 
is there something else in your system causing the -1 charge?


Adding a single Na+ to neutralize the charge may be appropriate, but that's up 
to you based on what's in your system (something else may be broken, but I just 
don't know).


-Justin


Sorry for tons of e-mails.
regards,

Payman


On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK! That's fine. But what if I do not have permissions to make such
changes in the itp files? Also, isn't that the case that when you define
That's why I said copy the force field files into your local directory.  Once 
there, you can modify them.



sth for the second time, grompp will take the second one? Sorry for mass
of e-mail!


That is only true in the case of .mdp files.

-Justin


Payman



On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?


I don't understand what you're saying you've already done.

The problem is this: when grompp attempts to assemble the .tpr file, it reads 
all of the information from the ffoplsaa*.itp files.  It finds the directives 
like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it finds a 
duplicate of these directives, it complains.  So when you #include your .itp 
file with new [atomtypes], it generates the error because it is a duplicate 
directive.  You have to include the new atom types in ffoplsaanb.itp in the 
[atomtypes] directive of this file.  The rest of the topology shouldn't cause a 
problem, just the [atomtypes] directive.


-Justin


Payman
  





On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
 
; This is an itp file to describe water's six-site model by H. Nada and

J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively

[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1   2   NO

[ atomtypes ]
;name   masscharge  ptype   c6  c12
OW  15.9994 0.0 A   0.3115  0.714845562
HW  1.00800 0.477   A   0.0673  0.11541
MW  0.000   -0.866  D   0.000.00
LW  0.00-0.044  D   0.000.00

[ moleculetype ]
;molnamenrexcl
SOL2

[ atoms ]
; nratomtyperesnr   residuename atomcgnrcharge
1   OW  1   SOL OW  1   0.0
2   HW  1  

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

When I look at the .top file generated by pdb2gmx, the last lines show
how this -0.99 is generated:

   442   opls_302 37ARG CZ138   0.64 12.011   ;
qtot -0.33
   443   opls_300 37ARGNH1139   -0.814.0067   ;
qtot -1.13
   444   opls_301 37ARG   HH11139   0.46  1.008   ;
qtot -0.67
   445   opls_301 37ARG   HH12139   0.46  1.008   ;
qtot -0.21
   446   opls_300 37ARGNH2140   -0.814.0067   ;
qtot -1.01
   447   opls_301 37ARG   HH21140   0.46  1.008   ;
qtot -0.55
   448   opls_301 37ARG   HH22140   0.46  1.008   ;
qtot -0.09
   449   opls_271 37ARG  C1410.7 12.011   ;
qtot 0.61
   450   opls_272 37ARG O1141   -0.815.9994   ;
qtot -0.19
   451   opls_272 37ARG O2141   -0.815.9994   ;
qtot -0.99

The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
simulation is supposed to be close to 7.0, I believe one of the
negatively-charged side chains needs to be neutralized. That's why I
think one Na+ might be helpful.

Payman


On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > OK! It worked! Thanks a lot again. But I have a final technical
> > question. After running grompp, it shows that my box has a net charge of
> > -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> > OK?! or even this 0.01 charge will cause me troubles?
> 
> Depending on the size of your system, rounding errors can occur.  It is 
> unusual 
> that the hundredths place would be showing this error.  Usually you'd get 
> something like 0.8 or something.  Your water topology has a zero net 
> charge; 
> is there something else in your system causing the -1 charge?
> 
> Adding a single Na+ to neutralize the charge may be appropriate, but that's 
> up 
> to you based on what's in your system (something else may be broken, but I 
> just 
> don't know).
> 
> -Justin
> 
> > Sorry for tons of e-mails.
> > regards,
> > 
> > Payman
> > 
> > 
> > On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! That's fine. But what if I do not have permissions to make such
> >>> changes in the itp files? Also, isn't that the case that when you define
> >> That's why I said copy the force field files into your local directory.  
> >> Once 
> >> there, you can modify them.
> >>
> >>> sth for the second time, grompp will take the second one? Sorry for mass
> >>> of e-mail!
> >>>
> >> That is only true in the case of .mdp files.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > I have done that already! I use my local copy to make my files. but how
> > can I get rid of this error? get into the oplsaanb.itp or include this
> > water model in the topology file before oplsaa.itp?
> >
>  I don't understand what you're saying you've already done.
> 
>  The problem is this: when grompp attempts to assemble the .tpr file, it 
>  reads 
>  all of the information from the ffoplsaa*.itp files.  It finds the 
>  directives 
>  like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it 
>  finds a 
>  duplicate of these directives, it complains.  So when you #include your 
>  .itp 
>  file with new [atomtypes], it generates the error because it is a 
>  duplicate 
>  directive.  You have to include the new atom types in ffoplsaanb.itp in 
>  the 
>  [atomtypes] directive of this file.  The rest of the topology shouldn't 
>  cause a 
>  problem, just the [atomtypes] directive.
> 
>  -Justin
> 
> > Payman
> >   
> >
> >
> >
> >
> > On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK!
> >>> here is the .itp file which I generated. I might upload it because it
> >>> has passed the initial tests.
> >>>  
> >>> ; This is an itp file to describe water's six-site model by H. Nada 
> >>> and
> >>> J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> >>> (2003)
> >>> ; This model is a combination of TIP4P and TIP5P. It has three LJ 
> >>> sites
> >>> and 3 Coulomb sites
> >>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> >>> 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> >>>
> >>> [ defaults ]
> >>> ; non-bondedtypecombrulegenpairsFudgeLJ
> >>> FudgeQQ N
> >>> 1   2   NO
> >>>
> >>> [ atomtypes ]
> >>> ;name   masscharge  ptype   c6  c12
> >>> OW  15.9994 0.0 A   0.3115  0.714845562
> >>> HW  1.00800 0.477   A   

Re: [gmx-users] Pressure swings during preliminary runs

[Justin A. Lemkul]

Warren Gallin wrote:

Justin,

OK, I see what's going on.

So then, since the instantaneous pressure values are so variable, is 
there a reason to implement pressure coupling for an MD run?




I guess if you're skeptical, check out the references for the coupling 
algorithms implemented in Gromacs.  Pressure affects a number of other 
observables, which, when averaged over time, represent the macroscopic 
properties (density, membrane properties, etc).  I've always found that, despite 
the fluctuation, the average pressure is correct.


-Justin


Warren

On 25-Aug-09, at 1:23 PM, Justin A. Lemkul wrote:



Warren Gallin wrote:

HI,
   I am trying to simulate the behavior of short peptides in an 
aqueous solution.
   When I look at the log of the progress of initial minimization 
runs and longer production runs I am seeing crazy variations in the 
pressure, including negative values and positive values well into the 
100's of bar.
   The temperature is equilibrating and stable, so I am thinking that 
I have missed some salient feature of the barostat.
   In one case I am not setting any of the relevant barostat 
parameters, relying on the default values to work - is there 
someplace where i can find waht the defaults values would be?


Defaults are applied by grompp; the mdout.mdp file will show all 
default values if you haven't specified them.  Otherwise, check out:


manual.gromacs.org

The behavior you are seeing is quite normal.  See here:

http://oldwiki.gromacs.org/index.php/pressure

-Justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

OK! It worked! Thanks a lot again. But I have a final technical
question. After running grompp, it shows that my box has a net charge of
-0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
OK?! or even this 0.01 charge will cause me troubles?


Depending on the size of your system, rounding errors can occur.  It is unusual 
that the hundredths place would be showing this error.  Usually you'd get 
something like 0.8 or something.  Your water topology has a zero net charge; 
is there something else in your system causing the -1 charge?


Adding a single Na+ to neutralize the charge may be appropriate, but that's up 
to you based on what's in your system (something else may be broken, but I just 
don't know).


-Justin


Sorry for tons of e-mails.
regards,

Payman


On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK! That's fine. But what if I do not have permissions to make such
changes in the itp files? Also, isn't that the case that when you define
That's why I said copy the force field files into your local directory.  Once 
there, you can modify them.



sth for the second time, grompp will take the second one? Sorry for mass
of e-mail!


That is only true in the case of .mdp files.

-Justin


Payman



On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?


I don't understand what you're saying you've already done.

The problem is this: when grompp attempts to assemble the .tpr file, it reads 
all of the information from the ffoplsaa*.itp files.  It finds the directives 
like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it finds a 
duplicate of these directives, it complains.  So when you #include your .itp 
file with new [atomtypes], it generates the error because it is a duplicate 
directive.  You have to include the new atom types in ffoplsaanb.itp in the 
[atomtypes] directive of this file.  The rest of the topology shouldn't cause a 
problem, just the [atomtypes] directive.


-Justin


Payman
  





On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
 
; This is an itp file to describe water's six-site model by H. Nada and

J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively

[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1   2   NO

[ atomtypes ]
;name   masscharge  ptype   c6  c12
OW  15.9994 0.0 A   0.3115  0.714845562
HW  1.00800 0.477   A   0.0673  0.11541
MW  0.000   -0.866  D   0.000.00
LW  0.00-0.044  D   0.000.00

[ moleculetype ]
;molnamenrexcl
SOL2

[ atoms ]
; nratomtyperesnr   residuename atomcgnrcharge
1   OW  1   SOL OW  1   0.0
2   HW  1   SOL HW1 1   0.477
3   HW  1   SOL HW2 1   0.477
4   MW  1   SOL MW  1   -0.866
5   LW  1   SOL LP1 1   -0.044
6   LW  1   SOL LP2 1   -0.044

[ settles ]
; OWfunctiondoh dhh
1   1   0.0980  0.15856

[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function
1
;
; site  fromfunctiona   b
4   1  2  3 1   0.199642536 0.199642536

; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds, a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site  from

Re: [gmx-users] Pressure swings during preliminary runs

[Warren Gallin]

Justin,

OK, I see what's going on.

	So then, since the instantaneous pressure values are so variable, is  
there a reason to implement pressure coupling for an MD run?


Warren

On 25-Aug-09, at 1:23 PM, Justin A. Lemkul wrote:



Warren Gallin wrote:

HI,
   I am trying to simulate the behavior of short peptides in an  
aqueous solution.
   When I look at the log of the progress of initial minimization  
runs and longer production runs I am seeing crazy variations in the  
pressure, including negative values and positive values well into  
the 100's of bar.
   The temperature is equilibrating and stable, so I am thinking  
that I have missed some salient feature of the barostat.
   In one case I am not setting any of the relevant barostat  
parameters, relying on the default values to work - is there  
someplace where i can find waht the defaults values would be?


Defaults are applied by grompp; the mdout.mdp file will show all  
default values if you haven't specified them.  Otherwise, check out:


manual.gromacs.org

The behavior you are seeing is quite normal.  See here:

http://oldwiki.gromacs.org/index.php/pressure

-Justin


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Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

OK! It worked! Thanks a lot again. But I have a final technical
question. After running grompp, it shows that my box has a net charge of
-0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
OK?! or even this 0.01 charge will cause me troubles?
Sorry for tons of e-mails.
regards,

Payman


On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > OK! That's fine. But what if I do not have permissions to make such
> > changes in the itp files? Also, isn't that the case that when you define
> 
> That's why I said copy the force field files into your local directory.  Once 
> there, you can modify them.
> 
> > sth for the second time, grompp will take the second one? Sorry for mass
> > of e-mail!
> > 
> 
> That is only true in the case of .mdp files.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> I have done that already! I use my local copy to make my files. but how
> >>> can I get rid of this error? get into the oplsaanb.itp or include this
> >>> water model in the topology file before oplsaa.itp?
> >>>
> >> I don't understand what you're saying you've already done.
> >>
> >> The problem is this: when grompp attempts to assemble the .tpr file, it 
> >> reads 
> >> all of the information from the ffoplsaa*.itp files.  It finds the 
> >> directives 
> >> like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it 
> >> finds a 
> >> duplicate of these directives, it complains.  So when you #include your 
> >> .itp 
> >> file with new [atomtypes], it generates the error because it is a 
> >> duplicate 
> >> directive.  You have to include the new atom types in ffoplsaanb.itp in 
> >> the 
> >> [atomtypes] directive of this file.  The rest of the topology shouldn't 
> >> cause a 
> >> problem, just the [atomtypes] directive.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>   
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > OK!
> > here is the .itp file which I generated. I might upload it because it
> > has passed the initial tests.
> >  
> > ; This is an itp file to describe water's six-site model by H. Nada and
> > J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> > (2003)
> > ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> > and 3 Coulomb sites
> > ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> > 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> >
> > [ defaults ]
> > ; non-bondedtypecombrulegenpairsFudgeLJ
> > FudgeQQ N
> > 1   2   NO
> >
> > [ atomtypes ]
> > ;name   masscharge  ptype   c6  c12
> > OW  15.9994 0.0 A   0.3115  0.714845562
> > HW  1.00800 0.477   A   0.0673  0.11541
> > MW  0.000   -0.866  D   0.000.00
> > LW  0.00-0.044  D   0.000.00
> >
> > [ moleculetype ]
> > ;molnamenrexcl
> > SOL2
> >
> > [ atoms ]
> > ; nratomtyperesnr   residuename atomcgnrcharge
> > 1   OW  1   SOL OW  1   0.0
> > 2   HW  1   SOL HW1 1   0.477
> > 3   HW  1   SOL HW2 1   0.477
> > 4   MW  1   SOL MW  1   -0.866
> > 5   LW  1   SOL LP1 1   -0.044
> > 6   LW  1   SOL LP2 1   -0.044
> >
> > [ settles ]
> > ; OWfunctiondoh dhh
> > 1   1   0.0980  0.15856
> >
> > [ dummies3 ]
> > ; These set of parameters are for M site which can be easily calculated
> > using TIP4P calculations from tip4p.itp
> > ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> > b*(r(i)-r(k))
> > ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> > Remember that OM is in the same direction of OH bonds.
> > ; Remember this site is in the same plane of OH bonds; so, its function
> > 1
> > ;
> > ; site  fromfunctiona   b
> > 4   1  2  3 1   0.199642536 0.199642536
> >
> > ; Now we define the position of L sites which can be obtained from
> > tip5p.itp
> > ; So, it will be described as dummy site 3out: r(v) = r(i) +
> > a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> > ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> > |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> > bonds, a minus sign is added. This part is similar to M s

Re: [gmx-users] Pressure swings during preliminary runs

[Justin A. Lemkul]

Warren Gallin wrote:

HI,

I am trying to simulate the behavior of short peptides in an aqueous 
solution.


When I look at the log of the progress of initial minimization runs 
and longer production runs I am seeing crazy variations in the pressure, 
including negative values and positive values well into the 100's of bar.


The temperature is equilibrating and stable, so I am thinking that I 
have missed some salient feature of the barostat.


In one case I am not setting any of the relevant barostat 
parameters, relying on the default values to work - is there someplace 
where i can find waht the defaults values would be?




Defaults are applied by grompp; the mdout.mdp file will show all default values 
if you haven't specified them.  Otherwise, check out:


manual.gromacs.org

The behavior you are seeing is quite normal.  See here:

http://oldwiki.gromacs.org/index.php/pressure

-Justin


In another case I am using the following settings in the .mdp file:

integrator  = md
nsteps  = 5
dt  = 0.002
nstlist = 10
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = v-rescale
tc-grps = protein non-protein
tau-t   = 0.1 0.1
ref-t   = 298 298
Pcoupl  = Berendsen
tau-p   = 1.0
compressibility = 1e-5 1e-5 1e-5 0 0 0
ref-p   = 1.0
nstenergy   = 100
define  = -DPOSRES


Can someone point me at some relevant information on how to 
troubleshoot large rapid pressure variations?


Thanks

Warren Gallin
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Pressure swings during preliminary runs

[Warren Gallin]

HI,

	I am trying to simulate the behavior of short peptides in an aqueous  
solution.


	When I look at the log of the progress of initial minimization runs  
and longer production runs I am seeing crazy variations in the  
pressure, including negative values and positive values well into the  
100's of bar.


	The temperature is equilibrating and stable, so I am thinking that I  
have missed some salient feature of the barostat.


	In one case I am not setting any of the relevant barostat parameters,  
relying on the default values to work - is there someplace where i can  
find waht the defaults values would be?


In another case I am using the following settings in the .mdp file:

integrator  = md
nsteps  = 5
dt  = 0.002
nstlist = 10
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = v-rescale
tc-grps = protein non-protein
tau-t   = 0.1 0.1
ref-t   = 298 298
Pcoupl  = Berendsen
tau-p   = 1.0
compressibility = 1e-5 1e-5 1e-5 0 0 0
ref-p   = 1.0
nstenergy   = 100
define  = -DPOSRES


	Can someone point me at some relevant information on how to  
troubleshoot large rapid pressure variations?


Thanks

Warren Gallin
___
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Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

Thanks!
I had misunderstood you! I thought you meant to modify them in the root
directory! My mistake! Thanks a lot. I will try to see what I can do.

Payman



On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > OK! That's fine. But what if I do not have permissions to make such
> > changes in the itp files? Also, isn't that the case that when you define
> 
> That's why I said copy the force field files into your local directory.  Once 
> there, you can modify them.
> 
> > sth for the second time, grompp will take the second one? Sorry for mass
> > of e-mail!
> > 
> 
> That is only true in the case of .mdp files.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> I have done that already! I use my local copy to make my files. but how
> >>> can I get rid of this error? get into the oplsaanb.itp or include this
> >>> water model in the topology file before oplsaa.itp?
> >>>
> >> I don't understand what you're saying you've already done.
> >>
> >> The problem is this: when grompp attempts to assemble the .tpr file, it 
> >> reads 
> >> all of the information from the ffoplsaa*.itp files.  It finds the 
> >> directives 
> >> like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it 
> >> finds a 
> >> duplicate of these directives, it complains.  So when you #include your 
> >> .itp 
> >> file with new [atomtypes], it generates the error because it is a 
> >> duplicate 
> >> directive.  You have to include the new atom types in ffoplsaanb.itp in 
> >> the 
> >> [atomtypes] directive of this file.  The rest of the topology shouldn't 
> >> cause a 
> >> problem, just the [atomtypes] directive.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>   
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > OK!
> > here is the .itp file which I generated. I might upload it because it
> > has passed the initial tests.
> >  
> > ; This is an itp file to describe water's six-site model by H. Nada and
> > J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> > (2003)
> > ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> > and 3 Coulomb sites
> > ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> > 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> >
> > [ defaults ]
> > ; non-bondedtypecombrulegenpairsFudgeLJ
> > FudgeQQ N
> > 1   2   NO
> >
> > [ atomtypes ]
> > ;name   masscharge  ptype   c6  c12
> > OW  15.9994 0.0 A   0.3115  0.714845562
> > HW  1.00800 0.477   A   0.0673  0.11541
> > MW  0.000   -0.866  D   0.000.00
> > LW  0.00-0.044  D   0.000.00
> >
> > [ moleculetype ]
> > ;molnamenrexcl
> > SOL2
> >
> > [ atoms ]
> > ; nratomtyperesnr   residuename atomcgnrcharge
> > 1   OW  1   SOL OW  1   0.0
> > 2   HW  1   SOL HW1 1   0.477
> > 3   HW  1   SOL HW2 1   0.477
> > 4   MW  1   SOL MW  1   -0.866
> > 5   LW  1   SOL LP1 1   -0.044
> > 6   LW  1   SOL LP2 1   -0.044
> >
> > [ settles ]
> > ; OWfunctiondoh dhh
> > 1   1   0.0980  0.15856
> >
> > [ dummies3 ]
> > ; These set of parameters are for M site which can be easily calculated
> > using TIP4P calculations from tip4p.itp
> > ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> > b*(r(i)-r(k))
> > ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> > Remember that OM is in the same direction of OH bonds.
> > ; Remember this site is in the same plane of OH bonds; so, its function
> > 1
> > ;
> > ; site  fromfunctiona   b
> > 4   1  2  3 1   0.199642536 0.199642536
> >
> > ; Now we define the position of L sites which can be obtained from
> > tip5p.itp
> > ; So, it will be described as dummy site 3out: r(v) = r(i) +
> > a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> > ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> > |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> > bonds, a minus sign is added. This part is similar to M site.
> > ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> > the magnitude of vector product of OH bonds.
> > ; 

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

OK! That's fine. But what if I do not have permissions to make such
changes in the itp files? Also, isn't that the case that when you define


That's why I said copy the force field files into your local directory.  Once 
there, you can modify them.



sth for the second time, grompp will take the second one? Sorry for mass
of e-mail!



That is only true in the case of .mdp files.

-Justin


Payman



On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?


I don't understand what you're saying you've already done.

The problem is this: when grompp attempts to assemble the .tpr file, it reads 
all of the information from the ffoplsaa*.itp files.  It finds the directives 
like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it finds a 
duplicate of these directives, it complains.  So when you #include your .itp 
file with new [atomtypes], it generates the error because it is a duplicate 
directive.  You have to include the new atom types in ffoplsaanb.itp in the 
[atomtypes] directive of this file.  The rest of the topology shouldn't cause a 
problem, just the [atomtypes] directive.


-Justin


Payman
  





On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
 
; This is an itp file to describe water's six-site model by H. Nada and

J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively

[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1   2   NO

[ atomtypes ]
;name   masscharge  ptype   c6  c12
OW  15.9994 0.0 A   0.3115  0.714845562
HW  1.00800 0.477   A   0.0673  0.11541
MW  0.000   -0.866  D   0.000.00
LW  0.00-0.044  D   0.000.00

[ moleculetype ]
;molnamenrexcl
SOL2

[ atoms ]
; nratomtyperesnr   residuename atomcgnrcharge
1   OW  1   SOL OW  1   0.0
2   HW  1   SOL HW1 1   0.477
3   HW  1   SOL HW2 1   0.477
4   MW  1   SOL MW  1   -0.866
5   LW  1   SOL LP1 1   -0.044
6   LW  1   SOL LP2 1   -0.044

[ settles ]
; OWfunctiondoh dhh
1   1   0.0980  0.15856

[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function
1
;
; site  fromfunctiona   b
4   1  2  3 1   0.199642536 0.199642536

; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds, a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site  fromfunctiona   b
c
5   1  2  3 4   -0.437172388-0.437172388
8.022961206
6   1  2  3 4   -0.437172388-0.437172388
-8.022961206

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

and here is the message I get from grompp:

Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File sixsitewater.itp, line 12
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---

I believe the original files of GROMACS need admin permissions which I
do not have on the cluste

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

OK! That's fine. But what if I do not have permissions to make such
changes in the itp files? Also, isn't that the case that when you define
sth for the second time, grompp will take the second one? Sorry for mass
of e-mail!

Payman



On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > I have done that already! I use my local copy to make my files. but how
> > can I get rid of this error? get into the oplsaanb.itp or include this
> > water model in the topology file before oplsaa.itp?
> > 
> 
> I don't understand what you're saying you've already done.
> 
> The problem is this: when grompp attempts to assemble the .tpr file, it reads 
> all of the information from the ffoplsaa*.itp files.  It finds the directives 
> like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it 
> finds a 
> duplicate of these directives, it complains.  So when you #include your .itp 
> file with new [atomtypes], it generates the error because it is a duplicate 
> directive.  You have to include the new atom types in ffoplsaanb.itp in the 
> [atomtypes] directive of this file.  The rest of the topology shouldn't cause 
> a 
> problem, just the [atomtypes] directive.
> 
> -Justin
> 
> > Payman
> >   
> > 
> > 
> > 
> > 
> > On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK!
> >>> here is the .itp file which I generated. I might upload it because it
> >>> has passed the initial tests.
> >>>  
> >>> ; This is an itp file to describe water's six-site model by H. Nada and
> >>> J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> >>> (2003)
> >>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> >>> and 3 Coulomb sites
> >>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> >>> 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> >>>
> >>> [ defaults ]
> >>> ; non-bondedtypecombrulegenpairsFudgeLJ
> >>> FudgeQQ N
> >>> 1   2   NO
> >>>
> >>> [ atomtypes ]
> >>> ;name   masscharge  ptype   c6  c12
> >>> OW  15.9994 0.0 A   0.3115  0.714845562
> >>> HW  1.00800 0.477   A   0.0673  0.11541
> >>> MW  0.000   -0.866  D   0.000.00
> >>> LW  0.00-0.044  D   0.000.00
> >>>
> >>> [ moleculetype ]
> >>> ;molnamenrexcl
> >>> SOL2
> >>>
> >>> [ atoms ]
> >>> ; nratomtyperesnr   residuename atomcgnrcharge
> >>> 1   OW  1   SOL OW  1   0.0
> >>> 2   HW  1   SOL HW1 1   0.477
> >>> 3   HW  1   SOL HW2 1   0.477
> >>> 4   MW  1   SOL MW  1   -0.866
> >>> 5   LW  1   SOL LP1 1   -0.044
> >>> 6   LW  1   SOL LP2 1   -0.044
> >>>
> >>> [ settles ]
> >>> ; OWfunctiondoh dhh
> >>> 1   1   0.0980  0.15856
> >>>
> >>> [ dummies3 ]
> >>> ; These set of parameters are for M site which can be easily calculated
> >>> using TIP4P calculations from tip4p.itp
> >>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> >>> b*(r(i)-r(k))
> >>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> >>> Remember that OM is in the same direction of OH bonds.
> >>> ; Remember this site is in the same plane of OH bonds; so, its function
> >>> 1
> >>> ;
> >>> ; site  fromfunctiona   b
> >>> 4   1  2  3 1   0.199642536 0.199642536
> >>>
> >>> ; Now we define the position of L sites which can be obtained from
> >>> tip5p.itp
> >>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
> >>> a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> >>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> >>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> >>> bonds, a minus sign is added. This part is similar to M site.
> >>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> >>> the magnitude of vector product of OH bonds.
> >>> ; This sites are tetrahedral sites; so, its function 4
> >>> ;
> >>> ; site  fromfunctiona   b
> >>> c
> >>> 5   1  2  3 4   -0.437172388-0.437172388
> >>> 8.022961206
> >>> 6   1  2  3 4   -0.437172388-0.437172388
> >>> -8.022961206
> >>>
> >>> [ exclusions ]
> >>> 1   2   3   4   5   6
> >>> 2   1   3   4   5   6
> >>> 3   1   2   4   5   6
> >>> 4   1   2   3   5   6
> >>> 5   1   2   3   4   6
> >>> 6   1   2   3   4   5
> >>>
> >>> and here is the message I get from gromp

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?



I don't understand what you're saying you've already done.

The problem is this: when grompp attempts to assemble the .tpr file, it reads 
all of the information from the ffoplsaa*.itp files.  It finds the directives 
like [defaults], [atomtypes], etc in a pre-defined order.  If, later, it finds a 
duplicate of these directives, it complains.  So when you #include your .itp 
file with new [atomtypes], it generates the error because it is a duplicate 
directive.  You have to include the new atom types in ffoplsaanb.itp in the 
[atomtypes] directive of this file.  The rest of the topology shouldn't cause a 
problem, just the [atomtypes] directive.


-Justin


Payman
  





On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
 
; This is an itp file to describe water's six-site model by H. Nada and

J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively

[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1   2   NO

[ atomtypes ]
;name   masscharge  ptype   c6  c12
OW  15.9994 0.0 A   0.3115  0.714845562
HW  1.00800 0.477   A   0.0673  0.11541
MW  0.000   -0.866  D   0.000.00
LW  0.00-0.044  D   0.000.00

[ moleculetype ]
;molnamenrexcl
SOL2

[ atoms ]
; nratomtyperesnr   residuename atomcgnrcharge
1   OW  1   SOL OW  1   0.0
2   HW  1   SOL HW1 1   0.477
3   HW  1   SOL HW2 1   0.477
4   MW  1   SOL MW  1   -0.866
5   LW  1   SOL LP1 1   -0.044
6   LW  1   SOL LP2 1   -0.044

[ settles ]
; OWfunctiondoh dhh
1   1   0.0980  0.15856

[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function
1
;
; site  fromfunctiona   b
4   1  2  3 1   0.199642536 0.199642536

; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds, a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site  fromfunctiona   b
c
5   1  2  3 4   -0.437172388-0.437172388
8.022961206
6   1  2  3 4   -0.437172388-0.437172388
-8.022961206

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

and here is the message I get from grompp:

Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File sixsitewater.itp, line 12
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---

I believe the original files of GROMACS need admin permissions which I
do not have on the cluster that I am currently using and I am not sure
if that might not cause troubles for other users. So, I thought how I
can keep the changes local.

Make a copy in your local directory; grompp will use these before looking for 
system-wide files.  As a general rule, whenever developing new parameters or 
adjusting files, do so locally before potentially messing yourself (or others) up :)


-Justin


Payman


On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?

Payman
  




On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > OK!
> > here is the .itp file which I generated. I might upload it because it
> > has passed the initial tests.
> >  
> > ; This is an itp file to describe water's six-site model by H. Nada and
> > J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> > (2003)
> > ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> > and 3 Coulomb sites
> > ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> > 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> > 
> > [ defaults ]
> > ; non-bondedtypecombrulegenpairsFudgeLJ
> > FudgeQQ N
> > 1   2   NO
> > 
> > [ atomtypes ]
> > ;name   masscharge  ptype   c6  c12
> > OW  15.9994 0.0 A   0.3115  0.714845562
> > HW  1.00800 0.477   A   0.0673  0.11541
> > MW  0.000   -0.866  D   0.000.00
> > LW  0.00-0.044  D   0.000.00
> > 
> > [ moleculetype ]
> > ;molnamenrexcl
> > SOL2
> > 
> > [ atoms ]
> > ; nratomtyperesnr   residuename atomcgnrcharge
> > 1   OW  1   SOL OW  1   0.0
> > 2   HW  1   SOL HW1 1   0.477
> > 3   HW  1   SOL HW2 1   0.477
> > 4   MW  1   SOL MW  1   -0.866
> > 5   LW  1   SOL LP1 1   -0.044
> > 6   LW  1   SOL LP2 1   -0.044
> > 
> > [ settles ]
> > ; OWfunctiondoh dhh
> > 1   1   0.0980  0.15856
> > 
> > [ dummies3 ]
> > ; These set of parameters are for M site which can be easily calculated
> > using TIP4P calculations from tip4p.itp
> > ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> > b*(r(i)-r(k))
> > ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> > Remember that OM is in the same direction of OH bonds.
> > ; Remember this site is in the same plane of OH bonds; so, its function
> > 1
> > ;
> > ; site  fromfunctiona   b
> > 4   1  2  3 1   0.199642536 0.199642536
> > 
> > ; Now we define the position of L sites which can be obtained from
> > tip5p.itp
> > ; So, it will be described as dummy site 3out: r(v) = r(i) +
> > a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> > ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> > |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> > bonds, a minus sign is added. This part is similar to M site.
> > ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> > the magnitude of vector product of OH bonds.
> > ; This sites are tetrahedral sites; so, its function 4
> > ;
> > ; site  fromfunctiona   b
> > c
> > 5   1  2  3 4   -0.437172388-0.437172388
> > 8.022961206
> > 6   1  2  3 4   -0.437172388-0.437172388
> > -8.022961206
> > 
> > [ exclusions ]
> > 1   2   3   4   5   6
> > 2   1   3   4   5   6
> > 3   1   2   4   5   6
> > 4   1   2   3   5   6
> > 5   1   2   3   4   6
> > 6   1   2   3   4   5
> > 
> > and here is the message I get from grompp:
> > 
> > Program grompp_d_mpi, VERSION 4.0.5
> > Source code file: topio.c, line: 415
> > 
> > Fatal error:
> > Syntax error - File sixsitewater.itp, line 12
> > Last line read:
> > '[ atomtypes ]'
> > Invalid order for directive atomtypes
> > ---
> > 
> > I believe the original files of GROMACS need admin permissions which I
> > do not have on the cluster that I am currently using and I am not sure
> > if that might not cause troubles for other users. So, I thought how I
> > can keep the changes local.
> > 
> 
> Make a copy in your local directory; grompp will use these before looking for 
> system-wide files.  As a general rule, whenever developing new parameters or 
> adjusting files, do so locally before potentially messing yourself (or 
> others) up :)
> 
> -Justin
> 
> > Payman
> > 
> > 
> > On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Hello,
> >>> Just a reminder that I had troubled with combination rules between my
> >>> water model and GROMACS forcefields. I fixed the problem by adjusting my
> >>> water model's parameters. BUT, now, I specified the new parameters in
> >>> my .itp file under

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
 
; This is an itp file to describe water's six-site model by H. Nada and

J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively

[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1   2   NO

[ atomtypes ]
;name   masscharge  ptype   c6  c12
OW  15.9994 0.0 A   0.3115  0.714845562
HW  1.00800 0.477   A   0.0673  0.11541
MW  0.000   -0.866  D   0.000.00
LW  0.00-0.044  D   0.000.00

[ moleculetype ]
;molnamenrexcl
SOL2

[ atoms ]
; nratomtyperesnr   residuename atomcgnrcharge
1   OW  1   SOL OW  1   0.0
2   HW  1   SOL HW1 1   0.477
3   HW  1   SOL HW2 1   0.477
4   MW  1   SOL MW  1   -0.866
5   LW  1   SOL LP1 1   -0.044
6   LW  1   SOL LP2 1   -0.044

[ settles ]
; OWfunctiondoh dhh
1   1   0.0980  0.15856

[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function
1
;
; site  fromfunctiona   b
4   1  2  3 1   0.199642536 0.199642536

; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds, a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site  fromfunctiona   b
c
5   1  2  3 4   -0.437172388-0.437172388
8.022961206
6   1  2  3 4   -0.437172388-0.437172388
-8.022961206

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

and here is the message I get from grompp:

Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File sixsitewater.itp, line 12
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---

I believe the original files of GROMACS need admin permissions which I
do not have on the cluster that I am currently using and I am not sure
if that might not cause troubles for other users. So, I thought how I
can keep the changes local.



Make a copy in your local directory; grompp will use these before looking for 
system-wide files.  As a general rule, whenever developing new parameters or 
adjusting files, do so locally before potentially messing yourself (or others) up :)


-Justin


Payman


On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Hello,
Just a reminder that I had troubled with combination rules between my
water model and GROMACS forcefields. I fixed the problem by adjusting my
water model's parameters. BUT, now, I specified the new parameters in
my .itp file under [ atomtype ] category and grompp makes errors out of
the orders. Now I am using OPLSaa. I suspect again the problem comes
from the presence of the second [atomtype ]. How can I keep my new
parameters and use them in my water model's itp file? Or should I change
these parameters in the OPLSaa.itp file? 
You can't have a second [atomtypes] directive.  You can add new parameters to 
ffoplsaanb.itp to account for the atom types you are implementing, though.


If you want anything more specific, you'll probably have to provide the topology 
file you're working with, as well as any actual error messages you're seeing.


-Justin


Regards,

Payman  











On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:

P

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
 
; This is an itp file to describe water's six-site model by H. Nada and
J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively

[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1   2   NO

[ atomtypes ]
;name   masscharge  ptype   c6  c12
OW  15.9994 0.0 A   0.3115  0.714845562
HW  1.00800 0.477   A   0.0673  0.11541
MW  0.000   -0.866  D   0.000.00
LW  0.00-0.044  D   0.000.00

[ moleculetype ]
;molnamenrexcl
SOL2

[ atoms ]
; nratomtyperesnr   residuename atomcgnrcharge
1   OW  1   SOL OW  1   0.0
2   HW  1   SOL HW1 1   0.477
3   HW  1   SOL HW2 1   0.477
4   MW  1   SOL MW  1   -0.866
5   LW  1   SOL LP1 1   -0.044
6   LW  1   SOL LP2 1   -0.044

[ settles ]
; OWfunctiondoh dhh
1   1   0.0980  0.15856

[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function
1
;
; site  fromfunctiona   b
4   1  2  3 1   0.199642536 0.199642536

; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds, a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site  fromfunctiona   b
c
5   1  2  3 4   -0.437172388-0.437172388
8.022961206
6   1  2  3 4   -0.437172388-0.437172388
-8.022961206

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

and here is the message I get from grompp:

Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File sixsitewater.itp, line 12
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---

I believe the original files of GROMACS need admin permissions which I
do not have on the cluster that I am currently using and I am not sure
if that might not cause troubles for other users. So, I thought how I
can keep the changes local.

Payman


On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Hello,
> > Just a reminder that I had troubled with combination rules between my
> > water model and GROMACS forcefields. I fixed the problem by adjusting my
> > water model's parameters. BUT, now, I specified the new parameters in
> > my .itp file under [ atomtype ] category and grompp makes errors out of
> > the orders. Now I am using OPLSaa. I suspect again the problem comes
> > from the presence of the second [atomtype ]. How can I keep my new
> > parameters and use them in my water model's itp file? Or should I change
> > these parameters in the OPLSaa.itp file? 
> 
> You can't have a second [atomtypes] directive.  You can add new parameters to 
> ffoplsaanb.itp to account for the atom types you are implementing, though.
> 
> If you want anything more specific, you'll probably have to provide the 
> topology 
> file you're working with, as well as any actual error messages you're seeing.
> 
> -Justin
> 
> > Regards,
> > 
> > Payman  
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
> >> Paymon Pirzadeh wrote:
> >>> I checked all the force-fields available in the GROAMCS. None of them
> >>> have the #2 combination rule which matches my water model! Any

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Hello,
Just a reminder that I had troubled with combination rules between my
water model and GROMACS forcefields. I fixed the problem by adjusting my
water model's parameters. BUT, now, I specified the new parameters in
my .itp file under [ atomtype ] category and grompp makes errors out of
the orders. Now I am using OPLSaa. I suspect again the problem comes
from the presence of the second [atomtype ]. How can I keep my new
parameters and use them in my water model's itp file? Or should I change
these parameters in the OPLSaa.itp file? 


You can't have a second [atomtypes] directive.  You can add new parameters to 
ffoplsaanb.itp to account for the atom types you are implementing, though.


If you want anything more specific, you'll probably have to provide the topology 
file you're working with, as well as any actual error messages you're seeing.


-Justin


Regards,

Payman  











On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:

Paymon Pirzadeh wrote:

I checked all the force-fields available in the GROAMCS. None of them
have the #2 combination rule which matches my water model! Any
alternatives (rather than changing my water model)?
A water model that isn't compatible with the model of the solutes isn't 
of any value, so it looks like you have put the cart before the horse.


Mark


On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

That was very helpful! But I realized a problem. The OPLSaa uses the
combination rule #3 in [ defaults ] while my water model uses #2. Now if
I comment out my water model's combination, I am not sure what I am
going to face! Any comments?

Then I would say that your water model's combination rule is inconsistent with 
the method of nonbonded calculations in OPLS.  It appears that the only 
difference between combination rules 2 and 3 comes when a specific interaction 
is not defined in the [nonbond_params] section.  The specifics of these 
combination rules are given in manual section 5.3.3.


-Justin


Payman




On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Well,
I changed the topology file of the system and manually typed the .itp of
my own water model. Just a reminder that I have used my own water
model's .itp file successfully in pure water systems. This .itp file
starts from [ defaults ] and contains all information needed. But when
it comes to grompp, the following error appears:

Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File sixsitewater.itp, line 6
Last line read:
'[ defaults ]'
Invalid order for directive defaults

The only time that [defaults] should appear is in the force field that you are 
calling (i.e., ffoplsaa.itp):


http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

-Justin


I am trying to use this water model with OPLSaa. what kind of directive
am I missing? 


Payman





On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Hello,
I am trying to use a different water model for my proteins (using oplsaa
force field). I use the .itp file which I developed, but pdb2gmx does
not accept it. I am a bit confused on how I can make my water model work
with OPLSaa. Based on what I saw from spc.itp or other samples, do I
need to change the names of my particles in my water .itp file by
including _FF_OPLS?
I don't know how pdb2gmx decides how to recognize water models; it may be 
hard-coded.  In any case, your atom types have to be consistent with OPLS 
standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file, 
you may not need it if OPLS is the only force field with which it will be used. 
  The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.


-Justin


Regards,

Payman 


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Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

Hello,
Just a reminder that I had troubled with combination rules between my
water model and GROMACS forcefields. I fixed the problem by adjusting my
water model's parameters. BUT, now, I specified the new parameters in
my .itp file under [ atomtype ] category and grompp makes errors out of
the orders. Now I am using OPLSaa. I suspect again the problem comes
from the presence of the second [atomtype ]. How can I keep my new
parameters and use them in my water model's itp file? Or should I change
these parameters in the OPLSaa.itp file? 
Regards,

Payman  










On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
> Paymon Pirzadeh wrote:
> > I checked all the force-fields available in the GROAMCS. None of them
> > have the #2 combination rule which matches my water model! Any
> > alternatives (rather than changing my water model)?
> 
> A water model that isn't compatible with the model of the solutes isn't 
> of any value, so it looks like you have put the cart before the horse.
> 
> Mark
> 
> > On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> That was very helpful! But I realized a problem. The OPLSaa uses the
> >>> combination rule #3 in [ defaults ] while my water model uses #2. Now if
> >>> I comment out my water model's combination, I am not sure what I am
> >>> going to face! Any comments?
> >>>
> >> Then I would say that your water model's combination rule is inconsistent 
> >> with 
> >> the method of nonbonded calculations in OPLS.  It appears that the only 
> >> difference between combination rules 2 and 3 comes when a specific 
> >> interaction 
> >> is not defined in the [nonbond_params] section.  The specifics of these 
> >> combination rules are given in manual section 5.3.3.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
>  Paymon Pirzadeh wrote:
> > Well,
> > I changed the topology file of the system and manually typed the .itp of
> > my own water model. Just a reminder that I have used my own water
> > model's .itp file successfully in pure water systems. This .itp file
> > starts from [ defaults ] and contains all information needed. But when
> > it comes to grompp, the following error appears:
> >
> > Program grompp_d_mpi, VERSION 4.0.5
> > Source code file: topio.c, line: 415
> >
> > Fatal error:
> > Syntax error - File sixsitewater.itp, line 6
> > Last line read:
> > '[ defaults ]'
> > Invalid order for directive defaults
> >
>  The only time that [defaults] should appear is in the force field that 
>  you are 
>  calling (i.e., ffoplsaa.itp):
> 
>  http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
> 
>  -Justin
> 
> > I am trying to use this water model with OPLSaa. what kind of directive
> > am I missing? 
> >
> > Payman
> >
> >
> >
> >
> >
> > On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Hello,
> >>> I am trying to use a different water model for my proteins (using 
> >>> oplsaa
> >>> force field). I use the .itp file which I developed, but pdb2gmx does
> >>> not accept it. I am a bit confused on how I can make my water model 
> >>> work
> >>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
> >>> need to change the names of my particles in my water .itp file by
> >>> including _FF_OPLS?
> >> I don't know how pdb2gmx decides how to recognize water models; it may 
> >> be 
> >> hard-coded.  In any case, your atom types have to be consistent with 
> >> OPLS 
> >> standards; as for whether or not you need the #ifdef _FF_OPLS in your 
> >> .itp file, 
> >> you may not need it if OPLS is the only force field with which it will 
> >> be used. 
> >>   The #ifdef blocks just prevent a GROMOS system from trying to 
> >> recognize OPLS, etc.
> >>
> >> -Justin
> >>
> >>> Regards,
> >>>
> >>> Payman 
> >>>
> >>> ___
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at http://www.gromacs.org/search before 
> >>> posting!
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> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>
> >>>
> > 
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Re: [gmx-users] Grompp error

[Justin A. Lemkul]

Cíntia C. Vequi-Suplicy wrote:

Hello,

I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dppc128.top > gromppzJXISa'cpp
' command is defined in the .mdp file
*
* Important: if you do not have a c-preprocessor installed, *
* you MUST run grompp with the "-pp" command line option*
* in place of the "-p" option.  *
*
processing topology...
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (dppc128.gro, 17365)
   does not match topology (dppc128.top, 0)
---

"One Cross Each" (Monty Python)

I don´t where the problem is, I've already checked the cpp compiler and
it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
topology file I have the following lines:



Have you tried the advice from grompp to use -pp instead of -p?

General advice for this problem can be found here:

http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

Also an option is to upgrade to the most recent version of Gromacs (4.0.5), 
which does not require cpp.


-Justin


;
;File 'dppc128.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Aug 18 10:02:52 2009
;
;This is your topology file
;Pure DPPC bilayer with 128 lipids and 3655 water molecules
;
; The force field files to be include
#include "ffoplsaa.itp"
; Include DPPC topology
#include "dppc.itp"
#include "lipid.itp"
#include "spc.itp"

[ molecules ]
; Compound   #mol
DPP  128
SOL  3655

If anyone can help It will be very nice,

Thank you very much so far,
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Grompp error

Hello,

I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dppc128.top > gromppzJXISa'cpp
' command is defined in the .mdp file
*
* Important: if you do not have a c-preprocessor installed, *
* you MUST run grompp with the "-pp" command line option*
* in place of the "-p" option.  *
*
processing topology...
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (dppc128.gro, 17365)
   does not match topology (dppc128.top, 0)
---

"One Cross Each" (Monty Python)

I don´t where the problem is, I've already checked the cpp compiler and
it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
topology file I have the following lines:

;
;File 'dppc128.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Aug 18 10:02:52 2009
;
;This is your topology file
;Pure DPPC bilayer with 128 lipids and 3655 water molecules
;
; The force field files to be include
#include "ffoplsaa.itp"
; Include DPPC topology
#include "dppc.itp"
#include "lipid.itp"
#include "spc.itp"

[ molecules ]
; Compound   #mol
DPP  128
SOL  3655

If anyone can help It will be very nice,

Thank you very much so far,
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University
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[gmx-users] QM/MM tutorial available?

[Ye MEI]

Dear Gromacs users,

Is there any QM/MM tutorials for gromacs 3.3.3 or 4.0.5 available on line?
I cannot find any tutorials that run smoothly with either 3.3.3 or 4.0.5.
Thank you in advance.

Ye MEI


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[gmx-users] Re: Regarding Gromacs problem

[Justin A. Lemkul]

Please do not send private emails asking for help.  I've said this dozens of 
times; it is much more beneficial to the community as a whole to post the 
gmx-users list, where discussions are archived for future use.  You also have a 
better chance of reaching someone who knows how to solve your problem.  I know I 
respond a lot, but I don't always have an answer, nor do I advertise myself as a 
private tutor.  Contribution to the list is voluntary, when I've got a few moments.


Your system is blowing up, a fairly common problem.  See here for general tips:

http://oldwiki.gromacs.org/index.php/blowing_up

rituraj purohit wrote:

Hello Justin..
 I am getting a problem during dynamics(position restrain) of pr.mdp,
 at first i given dt = 0.002 and for 200ps (because protein is very big
 having 1480 aa = 11058 atoms) shows an error called table size at 1.6
 ps. Then i changed it dt = 0.001 for 200ps, but again i had a same
 error at ~45 ps.
 So finally i giving dt = 0.0001 for 200 ps, now its moving fine..but
 steps become 20 lacks :(
 1) The correction which i done , is it ok?


You're probably just prolonging the inevitable; the system is not stable.


 2) Is error occurred (with dt = 0.002 & 0.001) due to big size of protein?


No; it is due to some physically unrealistic aspect of the model physics 
(unresolvable clashes, inappropriate parameters).  Size should not be a problem; 
people are simulating viral capsids nowadays.



 3) To do dynamics for such a big protein is rel event?


That's up to you.


 4) Is 200 ps enough for this protein? is their any relation between
 protein size and pre-equilibrium period ?



There is no standard rule, really.  To justify equilibration, your observables 
have to have converged (i.e., temperature, pressure, density, RMSD, etc).


-Justin


Please help me in this..

 Regards,
  Rituraj



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: water simulation

[Vitaly V. Chaban]

You shouldn't have [atomtypes] where you declared it below.


> Message: 2
> Date: Tue, 25 Aug 2009 16:35:49 +0530
> From: abhijit kayal 
> Subject: [gmx-users] water simulation
> To: gmx-users@gromacs.org
> Message-ID:
>        
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> With my grompp.mdp,topol.top and gonf.gro i gave the command and the output
> was
> [abhi...@scfbioserver gromacs]$ grompp -f grompp.mdp  -p topol.top -c
> conf.gro -o water.tpr
>                         :-)  G  R  O  M  A  C  S  (-:
>
> ---
> Program grompp, VERSION 4.0.4
> Source code file: topio.c, line: 415
>
> Fatal error:
> Syntax error - File topol.top, line 4
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> ---


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, cell.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===
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Re: [gmx-users] Normal mode analysis

[Justin A. Lemkul]

abhijit kayal wrote:

Hi,
 If I going to perform normal mode analysis of a protien 
molecule what are the changes have to be done in .mdp files
 


That's what the manual is for, as well as pertinent literature and textbooks 
describing the protocols.


-Justin


Abhijit Kayal
 IIT Delhi




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] water simulation

[Justin A. Lemkul]

abhijit kayal wrote:




---
Program grompp, VERSION 4.0.4
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File topol.top, line 4
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---


The topology file follows a specified format.  Refer to Chapter 5, especially 
Table 5.3 which spells out exactly which sections of the topology are mandatory, 
and the order they must be in.




"I believe in miracles cause I'm one" (The Ramones)

[abhi...@scfbioserver gromacs]$
 my topol.top file is
xirsfudgeLJ fudgeQQ
1   2   yes 0.5 0.5


At the very least, you're missing a [ defaults ] heading; otherwise these lines 
are incorrectly formatted.



[ atomtypes ]
;name  at.num   mass   charge   ptype   sigma   epsilon
  OW8   15.99940   0.000A   0.31660.65
  HW11.00800   0.000A   0.0E+00   0.0E+00






coulombtype  = Cut-off


Using cutoff for electrostatics is archaic, and the artefacts are well-known. 
Use something more modern like PME.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Normal mode analysis

[abhijit kayal]

Hi,
 If I going to perform normal mode analysis of a protien molecule
what are the changes have to be done in .mdp files
   Abhijit
Kayal
 IIT Delhi
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[gmx-users] water simulation

[abhijit kayal]

Hi,
With my grompp.mdp,topol.top and gonf.gro i gave the command and the output
was
[abhi...@scfbioserver gromacs]$ grompp -f grompp.mdp  -p topol.top -c
conf.gro -o water.tpr
 :-)  G  R  O  M  A  C  S  (-:

Gravel Rubs Often Many Awfully Cauterized Sores

:-)  VERSION 4.0.4  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  grompp  (-:

Option Filename  Type Description

  -f grompp.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c   conf.gro  InputStructure file: gro g96 pdb tpr tpb tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n  index.ndx  Input, Opt.  Index file
  -p  topol.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o  water.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: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input
processing
-[no]zerobool   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

Ignoring obsolete mdp entry 'cpp'
checking input for internal consistency...

NOTE 1 [file grompp.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

processing topology...

---
Program grompp, VERSION 4.0.4
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File topol.top, line 4
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---

"I believe in miracles cause I'm one" (The Ramones)
[abhi...@scfbioserver gromacs]$
 my topol.top file is
xirsfudgeLJ fudgeQQ
1   2   yes 0.5 0.5
[ atomtypes ]
;name  at.num   mass   charge   ptype   sigma   epsilon
  OW8   15.99940   0.000A   0.31660.65
  HW11.00800   0.000A   0.0E+00   0.0E+00

;---
; Definition of the SPC/E water model---
;
[ moleculetype ]
; molname   nrexcl
SOL 2
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1 OW  1SOL OW  1-0.8476
 2 HW  1SOLHW1  1 0.4238
 3 HW  1SOLHW2  1 0.4238
[ settles ]
; OWfunct   doh dhh
1   1   0.1 0.16330
[ exclusions ]
1   2   3
2   1   3
3   1   2
;---
; End of definition of the SPC/E water model
;---

[ system ]
Water SPC/E
[ molecules ]
SOL 216

the conf.gro file is
  203SOLHW1  608   1.821   0.322   0.817  0.8928  1.1548  0.7389
  203SOLHW2  609   1.875   0.440   0.718 -1.9604  0.3767 -1.7905
  204SOL OW  610   0.779   1.345   0.916  0.2112 -0.0070  0.2315
  204SOLHW1  611   0.686   1.338   0.954  0.8109 -1.6887  1.4414
  204SOLHW2  612   0.805   1.442   0.909 -2.0435  0.5275 -1.1795
  205SOL OW  613   1.718   1.114   0.507  0.2154 -0.1127 -0.1792
  205SOLHW1  614   1.755   1.098   0.416 -0.9406 -0.2600 -0.6191
  205SOLHW2  615   1.769   1.060   0.574 -1.8561 -3.6296 -1.3196
  206SOL OW  616   0.694   0.641   1.677  0.0172  0.0058 -0.2012
  206SOLHW1  617   0.784

Re: [gmx-users] water simulation

[Justin A. Lemkul]

abhijit kayal wrote:

Hi everyone,
   I am new to the GROMACS.In GROMACS there is a example of 
water(spc model).But  after the command grompp -the output file 
water.tpr should generate.But it is not giving the output.So what kind 
of changes have to be done in grompp.mdp,topol.top, files.Please reply.


No clue.  We can't get inside your head to know what's going on.  Your first 
resources should always be the wiki site:


http://oldwiki.gromacs.org

followed by searching the list archive for your problem:

http://oldwww.gromacs.org/swish-e/search/search2.php

If you cannot find an answer to your problem, then post a *complete* description 
of what's going on - include relevant input/output (exact command line issued, 
the actual error message you received, etc).  Until then, you won't get any 
useful advice.


-Justin


   Abhijit Kayal
IIT Delhi
 





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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] water simulation

[abhijit kayal]

Hi everyone,
   I am new to the GROMACS.In GROMACS there is a example of
water(spc model).But  after the command grompp -the output file water.tpr
should generate.But it is not giving the output.So what kind of changes have
to be done in grompp.mdp,topol.top, files.Please reply.
   Abhijit Kayal
IIT Delhi
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php