[gmx-users] Re: DNA-ligand interactions with AMBER

[Alan]

Please, take a look at acpypi.googlecode.com. I hope it can help you.

Alan

On Wed, May 13, 2009 at 06:12,   wrote:

> Subject: [gmx-users] DNA-ligand interactions with AMBER
>
> Dear Gromacs users
>
> I am simulating the interactions between ligands and DNA
> using GROMACS with the AMBER force field, as implemented with
> the AMBER PORT for GROMACS. Simulating DNA is actually
> very easy with this protocol, but for the ligand some
> problems arise. Until now we are constructing the
> topology manually, but this became complicated for large
> ligands. What is the best way to construct ligand
> topologies with AMBER parameters, for using with GROMACS,
> provided that we DO NOT have the AMBER package?
>
> Thank you very much in advance.
>
> Paulo Netz
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] Parallel installation core2 quad -mpi?

[Peyman Yamin]

Hello everyone,

I'm coming back to Gromacs. Before installing gromacs on our new SC I want to 
do it on my desktop running SuSe 11.1 on an Intel Core2 Quad Q6700 @2.66GHz 
CPU-arch.

Gromacs version 4.0.3
gmxtests version 4.0.4 

1. Are these compatible? I could find neither a testset for 4.0.3 nor a 
version 4.0.4 of gromacs!

2. The parallel installation (with --enable-mpi) leads to failure in all 
tests. Can I run MPI-parallel runs with lam on my cpu at all? lamboot is 
scared to be run by root and tests get some permission denied message for 
grompp when run otherwise. How is the whole OpenMP(I) story going on?

3. normal installation (without --enable-mpi) leads to failure in (complex 
only) "field", "tip4p" and "water". concerning pdb2gmx:

Error not all 45 pdb2gmx tests have been done successfully
Only 44 energies in the log file

however, -np 2 or 4 leads to a faster finishing  with everything t he same 
other than "only 0 energies in the log file"!

I'm wondering how does it all go parallel with no mpi?

Thanks in advance,
Peyman

P.S. Here are checkpot.out and checkvir.out for tip4p (test with no -np). 
Those of field and water are similar.

CHECKPOT.OUT

      
comparing energy file reference_d.edr and ener.edr

There are 32 terms in the energy files

There are 4 terms to compare in the energy files


Files read succesfully


CHECKVIR.OUT

  

comparing energy file reference_d.edr and ener.edr

There are 32 terms in the energy files

There are 17 terms to compare in the energy files

Vir-YX           step   0:      -88.6406,  step   0:     -86.8772
Vir-YZ           step   0:       6.84064,  step   0:      7.13434
Vir-ZX           step   0:      -54.0067,  step   0:     -52.9951
Vir-ZY           step   0:       6.84064,  step   0:      7.62177
Vir-XY           step   1:      -51.1246,  step   1:     -52.1106
Vir-XZ           step   1:      -46.6056,  step   1:     -46.1179
Vir-YX           step   1:      -51.1246,  step   1:     -50.5221
Vir-ZX           step   1:      -46.6056,  step   1:     -45.8405
Vir-YZ           step   2:       62.6018,  step   2:      61.8139
Vir-XZ           step   3:      -15.0763,  step   3:      -14.869
Vir-YX           step   3:      -9.43724,  step   3:     -8.38063
Vir-YZ           step   3:       83.9097,  step   3:      85.0938
Vir-ZX           step   3:      -15.0763,  step   3:     -13.9701
Vir-XY           step   4:       -13.916,  step   4:     -13.4319
Vir-XZ           step   4:       9.84575,  step   4:      10.1562
Vir-ZX           step   4:       9.84575,  step   4:      9.57457
Vir-ZY           step   4:         93.54,  step   4:      94.6497
Vir-XY           step   5:      -34.0429,  step   5:     -33.1563
Vir-XZ           step   5:       37.7852,  step   5:       38.673
Vir-YX           step   5:      -34.0429,  step   5:     -33.5621
Vir-YZ           step   5:       87.6469,  step   5:      88.7462
Vir-ZX           step   5:       37.7852,  step   5:       38.247
Vir-XZ           step   6:       64.9231,  step   6:      63.4369
Vir-YX           step   6:      -63.5388,  step   6:     -62.7892
Vir-ZX           step   6:       64.9231,  step   6:       65.691
Vir-ZY           step   6:       66.1302,  step   6:      64.6016
Vir-XY           step   7:      -93.5354,  step   7:     -92.5473
Vir-YZ           step   7:       32.4225,  step   7:      33.1803
Vir-ZX           step   7:       87.7836,  step   7:      88.6865
Vir-ZY           step   7:       32.4225,  step   7:      33.6332
Vir-YZ           step   8:      -8.59918,  step   8:     -8.42516
Vir-ZY           step   8:      -8.59918,  step   8:     -9.54873
Vir-ZX           step   9:       111.664,  step   9:       110.52
Vir-ZY           step   9:      -52.1883,  step   9:     -53.1597
Vir-YX           step  10:      -116.858,  step  10:     -115.312
Vir-YX           step  12:      -66.7999,  step  12:     -65.7083
Vir-XY           step  13:      -33.7437,  step  13:     -34.3992
Vir-YX           step  13:      -33.7437,  step  13:      -34.804
Vir-XY           step  14:     -0.682353,  step  14:    -0.966198
Vir-YX           step  14:     -0.682353,  step  14:    -0.299812
Vir-XY           step  15:       30.6329,  step  15:      31.6687
Vir-XY           step  16:       59.1005,  step  16:      60.6541
Vir-XY           step  17:        83.184,  step  17:      82.2528
Vir-YX           step  17:        83.184,  step  17:      82.3063
Vir-ZX           step  18:       138.834,  step  18:      140.581
Vir-XY           step  25:        43.465,  step  25:      44.0824
Vir-YX           step  25:        43.465,  step  25:      41.8879
Vir-XY           step  26:       18.5651,  step  26:      17.6458
Vir-YX           step  26:       18.5651,  step  26:      18.9277
Vir-XY           step  27:      -15.0441,  step  27:     -17.3579
Vir-YX           step  27:      -15.0441,  step  27:     -13.4185
Vir-ZY           step  27:      -168.308,  step  27:     -170.416
Vir-XY           step  28:      -57.8682,  ste

[gmx-users] problem in simulation of DNA-protein complex

[nitu sharma]

Dear all

I  am getting problem in running pdb2gmx command on
DNA_protein file . The prblem is

Program pdb2gmx, VERSION 4.0.3
Source code file: resall.c, line: 426

Fatal error:
Residue 'T' not found in residue topology database

So , actually I am unable to understand what should I do to solve this .

Is it possible to get DNA.itp file from anywhere .If anyone have Idea about
this please help me.

I really will be very thankful for him/her.

Nitu sharma
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Re: [gmx-users] Parallel installation core2 quad -mpi?

[Mark Abraham]

Peyman Yamin wrote:

Hello everyone,

I'm coming back to Gromacs. Before installing gromacs on our new SC I want to 
do it on my desktop running SuSe 11.1 on an Intel Core2 Quad Q6700 @2.66GHz 
CPU-arch.


Gromacs version 4.0.3
gmxtests version 4.0.4 

1. Are these compatible? I could find neither a testset for 4.0.3 nor a 
version 4.0.4 of gromacs!


Sort of. There are some problems with Buckingham LJ in 4.0.x such that 
quite a few tests seem to fail. 4.0.5 exists but there seems not to have 
been a formal announcement yet. See 
http://www.gromacs.org/content/view/79/98/ or the front page


gmxtest.pl also needs updating to work "out of the box". We've seen so 
many confused-new-user posts that were I in charge, I'd be tempted to 
take it down until it's been updated and proven to work correctly with 
the most recent release. :-) A test set is a good idea, but not if it 
doesn't succeed at its objective in the hands of a newbie!


2. The parallel installation (with --enable-mpi) leads to failure in all 
tests. Can I run MPI-parallel runs with lam on my cpu at all? lamboot is 
scared to be run by root and tests get some permission denied message for 
grompp when run otherwise. How is the whole OpenMP(I) story going on?


You need a functional MPI installation. Pretty much any flavour should 
interact fine with GROMACS 4.x, I understand.


3. normal installation (without --enable-mpi) leads to failure in (complex 
only) "field", "tip4p" and "water". concerning pdb2gmx:


Error not all 45 pdb2gmx tests have been done successfully
Only 44 energies in the log file


There's a known bug going on here that was fixed sometime since 4.0.3

however, -np 2 or 4 leads to a faster finishing  with everything t he same 
other than "only 0 energies in the log file"!


These flags will have no effect on a non-MPI GROMACS.


I'm wondering how does it all go parallel with no mpi?


It doesn't.

Mark
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Re: [gmx-users] problem in simulation of DNA-protein complex

[Mark Abraham]

nitu sharma wrote:

Dear all

I  am getting problem in running pdb2gmx command on 
DNA_protein file . The prblem is 


Program pdb2gmx, VERSION 4.0.3
Source code file: resall.c, line: 426

Fatal error:
Residue 'T' not found in residue topology database

So , actually I am unable to understand what should I do to solve this .

Is it possible to get DNA.itp file from anywhere .If anyone have Idea 
about this please help me.


Yes. Search the wiki for this error. Read chapter 5 of the manual. 
Describe your problem more fully. You haven't even told us your command 
line or forcefield :-) Read the page linked at the bottom of 
http://wiki.gromacs.org/index.php/Support


Mark
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Re: [gmx-users] Parallel installation core2 quad -mpi?

[Peyman Yamin]

Hey Mark, 
thanks for the swift reply. 
I installed 4.0.5 now. with the same testset it failes this time on some of 
the kernel tests though all pdb2gmx ones pass. 

As far as I understood, I should simply ignore it?

I didn't use --enable-mpi but when I run test script with -np 4, it does the 
job clearly faster! Well, I wonder!

Peyman




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Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
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Prof. Dr. Sebastian M. Schmidt
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Re: [gmx-users] Parallel installation core2 quad -mpi?

[Mark Abraham]

Peyman Yamin wrote:
Hey Mark, 
thanks for the swift reply. 
I installed 4.0.5 now. with the same testset it failes this time on some of 
the kernel tests though all pdb2gmx ones pass. 


As far as I understood, I should simply ignore it?


Probably. If there's a problem, it's probably not yours.

I didn't use --enable-mpi but when I run test script with -np 4, it does the 
job clearly faster! Well, I wonder!


If you look at the top of the .log files in the subdirectories you will 
see whether it was a parallel calculation. If so, then you must be 
calling some version of GROMACS other than the one you've compiled 
without --enable-mpi.


Mark
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Re: [gmx-users] simulation of DNA model

[Justin A. Lemkul]

nitu sharma wrote:

Dear all
  I want to ask one basic question i.e is it possible to 
do simulation of DNA model with gromacs ? If it possible which force 
field will be suitable for this?




Yes.  Check out the force field .rtp files to see which contain parameters for 
nucleic acids.  You may want the AMBER ports:


http://chemistry.csulb.edu/ffamber/

-Justin


I am waiting for yours reply.
thanks a lot in advance.

Nitu sharma




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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] reg MOPAC/gromacs installation

[vidhya sankar]

Dear sir/Madam  Thanks in Advance
  i am  sorry for asking the same question  again reg 
MOPAC/gromacs installation. i did dos2linux coversion in two different online 
sever but when i use output of one server i got the error as follows  when i 
type ./configure   command in command prompt
: command not found1: 
../configure: line 40: syntax error near unexpected token `LANG'
../configure: line 40: ` LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE 
LC_'DENTIFICATION \
 
 
but  when i use output of another server i got the following error  
 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
: command not foundissing: line 3: 
: command not foundissing: line 5: 
: command not foundissing: line 9: 
: command not foundissing: line 14: 
: command not foundissing: line 19: 
: command not foundissing: line 24: 
: command not foundissing: line 29: 
'root/mopac7-1.10/missing: line 47: syntax error near unexpected token `in
'root/mopac7-1.10/missing: line 47: `case "$1" in
configure: WARNING: `missing' script is too old or missing
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: error: cannot run /bin/sh ./config.sub
 


  Own a website.Get an unlimited package.Pay next to nothing.*Go to 
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[gmx-users] reg MOPAC/gromacs installation

[vidhya sankar]

Dear sir/Madam  Thanks in Advance
  i am  sorry for asking the same question  again reg 
MOPAC/gromacs installation. i did dos2linux coversion in two different online 
sever but when i use output of one server i got the error as follows  when i 
type ./configure   command in command prompt
: command not found1: 
../configure: line 40: syntax error near unexpected token `LANG'
../configure: line 40: ` LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE 
LC_'DENTIFICATION \
 
 
but  when i use output of another server i got the following error  
 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
: command not foundissing: line 3: 
: command not foundissing: line 5: 
: command not foundissing: line 9: 
: command not foundissing: line 14: 
: command not foundissing: line 19: 
: command not foundissing: line 24: 
: command not foundissing: line 29: 
'root/mopac7-1.10/missing: line 47: syntax error near unexpected token `in
'root/mopac7-1.10/missing: line 47: `case "$1" in
configure: WARNING: `missing' script is too old or missing
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: error: cannot run /bin/sh ./config.sub
 
 
 
 
 
 
 
 
 

s/Personal/justin


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Re: [gmx-users] reg MOPAC/gromacs installation

[Mark Abraham]

vidhya sankar wrote:

Dear sir/Madam  Thanks in Advance
  i am  sorry for asking the same question  
again reg MOPAC/gromacs installation. i did dos2linux coversion in two 
different online sever but when i use output of one server i got the 
error as follows  when i type ./configure   command in command prompt

*: command not found1: *
*./configure: line 40: syntax error near unexpected token `LANG'*
*./configure: line 40: ` LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE 
LC_CTYPE LC_'DENTIFICATION \*
** 
 
but  when i use output of another server i got the following error 
 
checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes
: command not foundissing: line 3:
: command not foundissing: line 5:
: command not foundissing: line 9:
: command not foundissing: line 14:
: command not foundissing: line 19:
: command not foundissing: line 24:
: command not foundissing: line 29:
'root/mopac7-1.10/missing: line 47: syntax error near unexpected token `in
'root/mopac7-1.10/missing: line 47: `case "$1" in
configure: WARNING: `missing' script is too old or missing
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: error: cannot run /bin/sh ./config.sub


Your shells and/or machines seem to be horribly old, broken or both. In 
extremis, re-install a new operating system and try again :-)


Mark
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[gmx-users] ? particles communicated to PME node...

[Pavel Semenyuk]

Dear gmx users,
I run lipid bilayer simulations in parallel (gromacs v4.0.2), and I have fatal 
error:

4 particles communicated to PME node 2 are more than a cell length out of the 
domain
decomposition cell of their charge group

How can I fix it? Thank you in advance

Best regards,
Pavel I. Semenyuk

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Re: [gmx-users] ? particles communicated to PME node...

[Mark Abraham]

Pavel Semenyuk wrote:

Dear gmx users,
I run lipid bilayer simulations in parallel (gromacs v4.0.2), and I have fatal 
error:

4 particles communicated to PME node 2 are more than a cell length out of the 
domain
decomposition cell of their charge group

How can I fix it? Thank you in advance


I suggest you start by upgrading to 4.0.5 in case it's caused by 
something that's been fixed since 4.0.2. See 
http://www.gromacs.org/content/view/181/132/ for release notes.


Mark
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[gmx-users] adding non-polar hydrogens

[Stefano Meliga]

Hello,

I would like to add non-polar hydrogens as well as the polar ones.
Does anybody know if that is possible?
I haven't found any related option of the function pdb2gmx.

Thanks,
Stefano.
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[gmx-users] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing

[maria goranovic]

Dear All,

I ran a POPC simuIation in gromacs 3.3.1 with the martini force field and it
ran fine. But I am getting the following error when I run it in gromacs
4.0.4. It seems there is some problem with the way the topology is built,
but I cannot find out what the problem is?




A list of missing interactions:
G96Angle of   2395 missing  1

Molecule type 'POPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms9   10   11  global  1933  1934  1935

---
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 5532 bonded interactions could not be calculated because some atoms
involved moved further apart than
 the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance
(1.2 nm), see option -rdd, for pair
s and tabulated bonds also see option -ddcheck
---
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Re: [gmx-users] adding non-polar hydrogens

[Justin A. Lemkul]

Stefano Meliga wrote:

Hello,

I would like to add non-polar hydrogens as well as the polar ones.
Does anybody know if that is possible?
I haven't found any related option of the function pdb2gmx.



protonate -h

-Justin


Thanks,
Stefano.
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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] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing

[XAvier Periole]

Don't know about the missing interactions ... never seen this in any  
of the

gmx versions using Martini ...

for the error you should increase the -rdd to 1.4/1.5 nm

On May 13, 2009, at 4:36 PM, maria goranovic wrote:


Dear All,

I ran a POPC simuIation in gromacs 3.3.1 with the martini force  
field and it ran fine. But I am getting the following error when I  
run it in gromacs 4.0.4. It seems there is some problem with the way  
the topology is built, but I cannot find out what the problem is?





A list of missing interactions:
G96Angle of   2395 missing  1

Molecule type 'POPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms9   10   11  global  1933  1934   
1935


---
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 5532 bonded interactions could not be calculated because  
some atoms involved moved further apart than
 the multi-body cut-off distance (1.2 nm) or the two-body cut-off  
distance (1.2 nm), see option -rdd, for pair

s and tabulated bonds also see option -ddcheck
---

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Re: [gmx-users] Re: DNA-ligand interactions with AMBER

[Paulo Netz]

Thank you very much!

Paulo Netz



On 5/13/09, Alan  wrote:
> Please, take a look at acpypi.googlecode.com. I hope it can help you.
>
> Alan
>
> On Wed, May 13, 2009 at 06:12,   wrote:
>
>> Subject: [gmx-users] DNA-ligand interactions with AMBER
>>
>> Dear Gromacs users
>>
>> I am simulating the interactions between ligands and DNA
>> using GROMACS with the AMBER force field, as implemented with
>> the AMBER PORT for GROMACS. Simulating DNA is actually
>> very easy with this protocol, but for the ligand some
>> problems arise. Until now we are constructing the
>> topology manually, but this became complicated for large
>> ligands. What is the best way to construct ligand
>> topologies with AMBER parameters, for using with GROMACS,
>> provided that we DO NOT have the AMBER package?
>>
>> Thank you very much in advance.
>>
>> Paulo Netz
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] Condensation analysis

[Jacob Spooner]

I am doing some simulations involving high pressure condensation of 
hydrocarbons.  I have read that Gromacs can be used for condensation analysis.  
I have been looking at the g_cluster and g_clustsize commands, and I think that 
they will be my tools.  My main question is that if I am using g_cluster to 
identify a condensation "droplet", will the Jarvis Patrick method be the one 
that I would choose?  My other concern is that I have misunderstood g_cluster 
completely and it will not do what I want. Any help and comments would be 
greatly appreciated.

Thanks
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[gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

[Manik Mayur]

Hi Users,

I constructed a .pdb file for TIP4P water model which I tried to convert to
.gro using pdb2gmx using:

$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p

with the choice of forcefield as 5 (OPLS-AA/L all-atom force field). After
conversion I found that the position of HW3(MW), the dummy atom is not the
same relative to OW, what I kept in the .pdb file. Even during the
conversion pdb2gmx gave warnings as "Warning: Long Bond (1773-1776 =".
My .pdb file goes like this:

ATOM   1773  OW  SOL   108  45.944  29.409  58.762  1.00  0.00
ATOM   1774  HW1 SOL   108  46.530  29.409  59.519  1.00  0.00
ATOM   1775  HW2 SOL   108  46.530  29.409  58.005  1.00  0.00
ATOM   1776  HW3  SOL   108  46.094  29.409  58.762  1.00  0.00

note that the OW - HW3 is 0.15 angs as it should be.

So why is pdb2gmx recalculating the co-ordinates of HW3? How is the OW-HW3
bond is getting stretched? Also, what should be the correct procedure for
the conversion?

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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Re: [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

[Justin A. Lemkul]

Manik Mayur wrote:

Hi Users,

I constructed a .pdb file for TIP4P water model which I tried to convert 
to .gro using pdb2gmx using:


$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p



There is no need to use pdb2gmx.

If you just need a TIP4P solvent box, one exists in the /share/top subdirectory 
of your Gromacs installation (tip4p.gro).


If you want to use your configuration, use editconf to convert it to .gro and 
#include "tip4p.itp" in your topology (which you can write by hand for a simple 
water system), or leave it as .pdb; Gromacs can use many different file formats 
for structures.


with the choice of forcefield as 5 (OPLS-AA/L all-atom force field). 
After conversion I found that the position of HW3(MW), the dummy atom is 
not the same relative to OW, what I kept in the .pdb file. Even during 
the conversion pdb2gmx gave warnings as "Warning: Long Bond (1773-1776 
=".


What values does it find? (... does not help)

Interestingly, if one runs pdb2gmx on the existing tip4p.gro that comes 
pre-installed, the program reports "Short bond" warnings.



My .pdb file goes like this:

ATOM   1773  OW  SOL   108  45.944  29.409  58.762  1.00  0.00
ATOM   1774  HW1 SOL   108  46.530  29.409  59.519  1.00  0.00
ATOM   1775  HW2 SOL   108  46.530  29.409  58.005  1.00  0.00
ATOM   1776  HW3  SOL   108  46.094  29.409  58.762  1.00  0.00

note that the OW - HW3 is 0.15 angs as it should be.

So why is pdb2gmx recalculating the co-ordinates of HW3? How is the 
OW-HW3 bond is getting stretched? Also, what should be the correct 
procedure for the conversion?




The residue name "SOL" is interpreted as "HOH," or a three-point water molecule. 
 OPLS calls tip4p HO4 (per the .rtp file).  This could be a potential source of 
error.


-Justin


Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




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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] Problem with pdb2gmx when used with OPLS and TIP4P

[Manik Mayur]

On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul  wrote:

>
>
> Manik Mayur wrote:
>
>> Hi Users,
>>
>> I constructed a .pdb file for TIP4P water model which I tried to convert
>> to .gro using pdb2gmx using:
>>
>> $ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p
>>
>>
> There is no need to use pdb2gmx.
>
> If you just need a TIP4P solvent box, one exists in the /share/top
> subdirectory of your Gromacs installation (tip4p.gro).
>

Thanks for the reply. I needed to use pdb2gmx as it automatically checks for
errors in the configuration file. Moreover apart from water, my system has
silicon walls enclosing water.

If you want to use your configuration, use editconf to convert it to .gro
> and #include "tip4p.itp" in your topology (which you can write by hand for a
> simple water system), or leave it as .pdb; Gromacs can use many different
> file formats for structures.


yes, editconf will convert it to .gro but I was wondering why pdb2gmx is
behaving in such unexpected manner?


>  with the choice of forcefield as 5 (OPLS-AA/L all-atom force field). After
>> conversion I found that the position of HW3(MW), the dummy atom is not the
>> same relative to OW, what I kept in the .pdb file. Even during the
>> conversion pdb2gmx gave warnings as "Warning: Long Bond (1773-1776 =".
>>
>
> What values does it find? (... does not help)
>

e.g.
Warning: Long Bond (8637-8640 = 8.73449 nm)
 .. and so on for many more pairs (all ~8 nm)

Interestingly, if one runs pdb2gmx on the existing tip4p.gro that comes
> pre-installed, the program reports "Short bond" warnings.
>
>  My .pdb file goes like this:
>> 
>> ATOM   1773  OW  SOL   108  45.944  29.409  58.762  1.00  0.00
>> ATOM   1774  HW1 SOL   108  46.530  29.409  59.519  1.00  0.00
>> ATOM   1775  HW2 SOL   108  46.530  29.409  58.005  1.00  0.00
>> ATOM   1776  HW3  SOL   108  46.094  29.409  58.762  1.00  0.00
>> 
>> note that the OW - HW3 is 0.15 angs as it should be.
>>
>> So why is pdb2gmx recalculating the co-ordinates of HW3? How is the OW-HW3
>> bond is getting stretched? Also, what should be the correct procedure for
>> the conversion?
>>
>>
> The residue name "SOL" is interpreted as "HOH," or a three-point water
> molecule.  OPLS calls tip4p HO4 (per the .rtp file).  This could be a
> potential source of error.
>

with "-water tip4p" in pdb2gmx, SOL is interpreted as HO4, the default one
however is HOH.

Thanks,

-Justin
>
>  Thanks,
>>
>> Manik Mayur
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> INDIA
>>
>>
>> 
>>
>> ___
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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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] Problem with pdb2gmx when used with OPLS and TIP4P

[Justin A. Lemkul]

Manik Mayur wrote:
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul > wrote:




Manik Mayur wrote:

Hi Users,

I constructed a .pdb file for TIP4P water model which I tried to
convert to .gro using pdb2gmx using:

$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p


There is no need to use pdb2gmx.

If you just need a TIP4P solvent box, one exists in the /share/top
subdirectory of your Gromacs installation (tip4p.gro).


Thanks for the reply. I needed to use pdb2gmx as it automatically checks 
for errors in the configuration file. Moreover apart from water, my 
system has silicon walls enclosing water.




OK, then that makes more sense.


If you want to use your configuration, use editconf to convert it to
.gro and #include "tip4p.itp" in your topology (which you can write
by hand for a simple water system), or leave it as .pdb; Gromacs can
use many different file formats for structures.


yes, editconf will convert it to .gro but I was wondering why pdb2gmx is 
behaving in such unexpected manner?



with the choice of forcefield as 5 (OPLS-AA/L all-atom force
field). After conversion I found that the position of HW3(MW),
the dummy atom is not the same relative to OW, what I kept in
the .pdb file. Even during the conversion pdb2gmx gave warnings
as "Warning: Long Bond (1773-1776 =".


What values does it find? (... does not help)


e.g.
Warning: Long Bond (8637-8640 = 8.73449 nm)
 .. and so on for many more pairs (all ~8 nm)

Interestingly, if one runs pdb2gmx on the existing tip4p.gro that
comes pre-installed, the program reports "Short bond" warnings.


My .pdb file goes like this:

ATOM   1773  OW  SOL   108  45.944  29.409  58.762  1.00  0.00
ATOM   1774  HW1 SOL   108  46.530  29.409  59.519  1.00  0.00
ATOM   1775  HW2 SOL   108  46.530  29.409  58.005  1.00  0.00
ATOM   1776  HW3  SOL   108  46.094  29.409  58.762  1.00  0.00

note that the OW - HW3 is 0.15 angs as it should be.



The above is example is incorrect.  You have an extra space between HW3 and SOL, 
which (when I run pdb2gmx on it), generates the long bond warnings.  Check your 
.pdb file format and try again.


-Justin


So why is pdb2gmx recalculating the co-ordinates of HW3? How is
the OW-HW3 bond is getting stretched? Also, what should be the
correct procedure for the conversion?


The residue name "SOL" is interpreted as "HOH," or a three-point
water molecule.  OPLS calls tip4p HO4 (per the .rtp file).  This
could be a potential source of error.


with "-water tip4p" in pdb2gmx, SOL is interpreted as HO4, the default 
one however is HOH.


Thanks,

-Justin

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




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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] Problem with pdb2gmx when used with OPLS and TIP4P

[Manik Mayur]

On Thu, May 14, 2009 at 1:56 AM, Justin A. Lemkul  wrote:

>
>
> Manik Mayur wrote:
>
>> On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Manik Mayur wrote:
>>
>>Hi Users,
>>
>>I constructed a .pdb file for TIP4P water model which I tried to
>>convert to .gro using pdb2gmx using:
>>
>>$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p
>>
>>
>>There is no need to use pdb2gmx.
>>
>>If you just need a TIP4P solvent box, one exists in the /share/top
>>subdirectory of your Gromacs installation (tip4p.gro).
>>
>>
>> Thanks for the reply. I needed to use pdb2gmx as it automatically checks
>> for errors in the configuration file. Moreover apart from water, my system
>> has silicon walls enclosing water.
>>
>>
> OK, then that makes more sense.
>
> If you want to use your configuration, use editconf to convert it to
>>.gro and #include "tip4p.itp" in your topology (which you can write
>>by hand for a simple water system), or leave it as .pdb; Gromacs can
>>use many different file formats for structures.
>>
>>
>> yes, editconf will convert it to .gro but I was wondering why pdb2gmx is
>> behaving in such unexpected manner?
>>
>>
>>with the choice of forcefield as 5 (OPLS-AA/L all-atom force
>>field). After conversion I found that the position of HW3(MW),
>>the dummy atom is not the same relative to OW, what I kept in
>>the .pdb file. Even during the conversion pdb2gmx gave warnings
>>as "Warning: Long Bond (1773-1776 =".
>>
>>
>>What values does it find? (... does not help)
>>
>>
>> e.g.
>> Warning: Long Bond (8637-8640 = 8.73449 nm)
>>  .. and so on for many more pairs (all ~8 nm)
>>
>>Interestingly, if one runs pdb2gmx on the existing tip4p.gro that
>>comes pre-installed, the program reports "Short bond" warnings.
>>
>>
>>My .pdb file goes like this:
>>
>>ATOM   1773  OW  SOL   108  45.944  29.409  58.762  1.00  0.00
>>ATOM   1774  HW1 SOL   108  46.530  29.409  59.519  1.00  0.00
>>ATOM   1775  HW2 SOL   108  46.530  29.409  58.005  1.00  0.00
>>ATOM   1776  HW3  SOL   108  46.094  29.409  58.762  1.00  0.00
>>
>>note that the OW - HW3 is 0.15 angs as it should be.
>>
>>
> The above is example is incorrect.  You have an extra space between HW3 and
> SOL, which (when I run pdb2gmx on it), generates the long bond warnings.
>  Check your .pdb file format and try again.
>

Indeed the format was the issue, thanks for the help.

-Justin
>
> So why is pdb2gmx recalculating the co-ordinates of HW3? How is
>>the OW-HW3 bond is getting stretched? Also, what should be the
>>correct procedure for the conversion?
>>
>>
>>The residue name "SOL" is interpreted as "HOH," or a three-point
>>water molecule.  OPLS calls tip4p HO4 (per the .rtp file).  This
>>could be a potential source of error.
>>
>>
>> with "-water tip4p" in pdb2gmx, SOL is interpreted as HO4, the default one
>> however is HOH.
>>
>> Thanks,
>>
>>-Justin
>>
>>Thanks,
>>
>>Manik Mayur
>>Graduate student
>>Microfluidics Lab
>>Dept. of Mechanical Engg.
>>IIT Kharagpur
>>INDIA
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
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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
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
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>>posting!
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>>
>> 
>>
>> __

[gmx-users] What becomes of kinetic energy in local minima?

[yutong . zhao]

Hi Gmx,


I often hear the notion that "simulations" get stuck in local minima  
(for potential energy I assume), how come? What happens to the  
"kinetic energy" that is supposed to kick the system out of local  
minima? (ie. when I roll a marble down a dip it tends to come out so  
long as there's no friction. If the barrier is too high then wouldn't  
the system would sort of "oscillate" in the well? How does GMX treat  
KE loss via micromolecular friction?



Yutong Zhao

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[gmx-users] Where are the good tutorials?

[Joseph Johnson]

Are there any good tutorials that start from the very beginning, like assuming 
you only have a .pdb file?  It seems that most of the tutorials I've found have 
already generated the files you need and then all you have to do is punch in 
some commands.  Where can I learn to actually write the molecular dynamics 
input file and all that good stuff?

Thanks for your time and help,
Casey

_
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http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009___
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Re: [gmx-users] Where are the good tutorials?

[Justin A. Lemkul]

There are many:

http://wiki.gromacs.org/index.php/Tutorials

-Justin

Joseph Johnson wrote:
Are there any good tutorials that start from the very beginning, like 
assuming you only have a .pdb file?  It seems that most of the tutorials 
I've found have already generated the files you need and then all you 
have to do is punch in some commands.  Where can I learn to actually 
write the molecular dynamics input file and all that good stuff?


Thanks for your time and help,
Casey


Windows Live™: Keep your life in sync. Check it out. 






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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] problem in simulation of DNA-protein complex

[Dallas B. Warren]

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_
residue_topology_database

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma
Sent: Wednesday, 13 May 2009 5:25 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] problem in simulation of DNA-protein complex

 

Dear all

I  am getting problem in running pdb2gmx command on
DNA_protein file . The prblem is

Program pdb2gmx, VERSION 4.0.3
Source code file: resall.c, line: 426

Fatal error:
Residue 'T' not found in residue topology database

So , actually I am unable to understand what should I do to solve this .

Is it possible to get DNA.itp file from anywhere .If anyone have Idea
about this please help me.

I really will be very thankful for him/her.

Nitu sharma

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Re: [gmx-users] Where are the good tutorials?

[Rodrigo faccioli]

The Gromacs tutorial is a good place for us who is stating. Another place is
the Gromacs wiki which has a beginner section (
http://wiki.gromacs.org/index.php/Beginners). In this local, it's possible
you to see some videos.

I suggest for you read the online manual where has the flow chart and get
started sections (
http://www.gromacs.org/component/option,com_wrapper/Itemid,192/).

Regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Wed, May 13, 2009 at 7:24 PM, Joseph Johnson wrote:

>  Are there any good tutorials that start from the very beginning, like
> assuming you only have a .pdb file?  It seems that most of the tutorials
> I've found have already generated the files you need and then all you have
> to do is punch in some commands.  Where can I learn to actually write the
> molecular dynamics input file and all that good stuff?
>
> Thanks for your time and help,
> Casey
>
> --
> Windows Live™: Keep your life in sync. Check it 
> out.
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.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.
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>
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Re: [gmx-users] ? particles communicated to PME node...

[Pavel Semenyuk]

Thanks for quick answer.

But I'd faced another problem. When I compile gromacs 4.0.5, it crash with 
error "Cannot
find fftw3f library", instead of my FFTW is in single precision, and I'd 
exported to
CPPFLAGS and LDFLAGS real paths for libs. What is reason?
Thanks for help..

Best regards,
Pavel I. Semenyuk

Mark Abraham wrote: 
>Pavel Semenyuk wrote:
>Dear gmx users,
>I run lipid bilayer simulations in parallel (gromacs v4.0.2), and I have 
> fatal 
>error:
>4 particles communicated to PME node 2 are more than a cell length out of 
> the 
>domain
>decomposition cell of their charge group
>How can I fix it? Thank you in advance
>I suggest you start by upgrading to 4.0.5 in case it's caused by something 
>that's been
>fixed since 4.0.2. See http://www.gromacs.org/content/view/181/132/ for 
>release notes.
>Mark

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Re: [gmx-users] ? particles communicated to PME node...

[Justin A. Lemkul]

Pavel Semenyuk wrote:

Thanks for quick answer.

But I'd faced another problem. When I compile gromacs 4.0.5, it crash with error 
"Cannot
find fftw3f library", instead of my FFTW is in single precision, and I'd 
exported to
CPPFLAGS and LDFLAGS real paths for libs. What is reason?
Thanks for help..



Then you've probably made a mistake specifying those particular locations.  If 
you compiled Gromacs successfully before, and have made no pertinent changes to 
the locations of these necessary headers/libraries, then it's time to check your 
procedure carefully.


-Justin


Best regards,
Pavel I. Semenyuk

Mark Abraham wrote: 

Pavel Semenyuk wrote:
   Dear gmx users,
   I run lipid bilayer simulations in parallel (gromacs v4.0.2), and I have fatal 
   error:
   4 particles communicated to PME node 2 are more than a cell length out of the 
   domain

   decomposition cell of their charge group
   How can I fix it? Thank you in advance
I suggest you start by upgrading to 4.0.5 in case it's caused by something 
that's been
fixed since 4.0.2. See http://www.gromacs.org/content/view/181/132/ for release 
notes.
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] What becomes of kinetic energy in local minima?

[Mark Abraham]

yutong.z...@utoronto.ca wrote:

Hi Gmx,


I often hear the notion that "simulations" get stuck in local minima 
(for potential energy I assume), how come? What happens to the "kinetic 
energy" that is supposed to kick the system out of local minima? (ie. 
when I roll a marble down a dip it tends to come out so long as there's 
no friction. If the barrier is too high then wouldn't the system would 
sort of "oscillate" in the well? 


Yes, that's exactly what can happen. Dynamical simulations can get 
trapped in a well if its depth is a suitable multiple of kT.


How does GMX treat KE loss via 
micromolecular friction?


There isn't any. MDS integrate Newton's laws. Under constant-energy 
conditions (NVE), energy can only convert from form to form. Under 
constant-temperature conditions (NVT, NPT), velocities are manipulated 
to keep the average T near a value.


Mark
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[gmx-users] problem in DNA simulation

[nitu sharma]

Dear Mark

  Thanks for your kind reply . Actually I am just starting the
simulation of DnA-protein complex using gromacs. I got the  amber charged
force field ( to find DNA residues) from golovin_at_genebee.msu.su" and "
burnnick_u_at_rambler.ru" this site . The name of force field is ffoplsaano
.

BY using this I given the command like this-
 pdb2gmx -f dbd.pdb -o dbd.gro -p dbd.top -i dbd.itp -ff oplsaano

Then I am getting error like this-

Program pdb2gmx, VERSION 4.0.3
Source code file: h_db.c, line: 96

Fatal error:
Error in hdb file ffoplsaano.hdb:
Wrong number of control atoms (2 iso 3) on line:
1   1   N   -C  CA

Can u please help me in solving this problem.?
What does mean 2 iso 3?

Nitu Sharma
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RE: [gmx-users] problem in DNA simulation

[Dallas B. Warren]

Exact same question was answered just last month .
http://www.gromacs.org/pipermail/gmx-users/2009-April/040974.html

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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