date:20130317

RE: [gmx-users] covalent binding- Improper Dih

2013-03-17 Thread Emanuel Birru

Hi Jeremy,

It is hard to tell you what goes wrong from the information you gave us, but I 
suspect form the error message that the multiplicity that you used for the 
dihedral is wrong (the program is expecting 3 or 6 but you put 2 as 
multiplicity). Check it in the bonded itp file whether it is right. 

If you put what kind of force field you use, give us you itp or top file and 
etc, it would be easy to trace the problem. 

Cheers,
Eb

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Yongliang Yang
Sent: Monday, 18 March 2013 4:44 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] covalent binding- Improper Dih

Dear Gromacs users,

We tried to simulate a protein-ligand covalent binding by Gromacs. The covalent 
bond was formed between a Cys and the Michael acceptor struture of the small 
molecule. We had generated a itp file for the small molecule by using PRODRG2 
and converted it to rtp file. Unfortunately, the error message says: <>. We guess something was messed up in our rtp file. Could anybody be so 
kind to help?  Part of the rtp file was posted below. Any input are welcomed. 
Many thanks!

Cheers

Jeremy Yang


<>
--
  [ impropers ]
  CAD  OAX  CAB  CAG   0.000   167.4
  CAB  CAD  CAA  HAB   0.000   167.4
  CAG  CAE  OAY  CAD   0.000   167.4
  CAE  CAG  CAC  HAE   0.000   167.4
  CAC  CAE  CAA  HAC   0.000   167.4
  CAA  CAF  CAC  CAB   0.000   167.4
  CAM  CAQ  OAW  CAH   0.000   167.4
  CAT  CAQ  OAV  CAU   0.000   167.4
  CAN  CAO  CAK  CAL   0.000   167.4
  CAL  CAN  CAJ  HAL   0.000   167.4
  CAK  CAN  CAI  HAK   0.000   167.4
  CAI  CAK  CAS  HAI   0.000   167.4
  CAS  CAI  OAZ  CAJ   0.000   167.4
  CAJ  CAL  OBA  CAS   0.000   167.4
  CAN  CAL  CAJ  CAS   0.000   209.3
  CAL  CAJ  CAS  CAI   0.000   209.3
  CAJ  CAS  CAI  CAK   0.000   209.3
  CAS  CAI  CAK  CAN   0.000   209.3
  CAI  CAK  CAN  CAL   0.000   209.3
  CAK  CAN  CAL  CAJ   0.000   209.3
  CAD  CAB  CAA  CAC   0.000   209.3
  CAB  CAA  CAC  CAE   0.000   209.3
  CAA  CAC  CAE  CAG   0.000   209.3
  CAC  CAE  CAG  CAD   0.000   209.3
  CAE  CAG  CAD  CAB   0.000   209.3
  CAG  CAD  CAB  CAA   0.000   209.3
  [ dihedrals ]
  CAG  CAD  OAX  CAP 180.00016.7 2
  CAD  CAG  OAY  HAY 180.000 7.1 2
  CAH  CAF  CAA  CAB 180.000 5.9 2
  CAM  CAH  CAF  CAA 180.000 5.9 2
  CAQ  CAM  CAH  CAF 180.000 5.9 2
  CAT  CAQ  CAM  CAH   0.000 1.0 6
  CAM  CAQ  CAT  CAU   0.000 1.0 6
  CAO  CAU  CAT  CAQ 180.000 5.9 2
  CAN  CAO  CAU  CAT 180.000 5.9 2
  CAK  CAN  CAO  CAU 180.000 5.9 2
  CAI  CAS  OAZ  HAZ 180.000 7.1 2
  CAL  CAJ  OBA  CAR 180.00016.7 2
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[gmx-users] [Fwd: implicit solvation]

2013-03-17 Thread preetichoudhary

 Original Message 
Subject: implicit solvation
From:preetichoudh...@iisermohali.ac.in
Date:Fri, March 15, 2013 1:58 pm
To:  gmx-users@gromacs.org
--

hi,
I am trying to simulate a 50 residue protein in implicit water.Can anyone
tell me that why we usually set the cuttoff to be 0.
coulombtype = Cut-off
vdwtype = Cut-off
nstype = grid
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0.
I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain
why this is being done.
Also we dont need to do nvt and npt equlibration here.We dont neutralise
our system too.But it keeps on showing in note:
NOTE 1 [file topol.top, line 7412]:
  System has non-zero total charge: -2.00
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

Correct me if I am wrong.
Also while doing production run,I am getting this error:-
WARNING 1 [file topol.top, line 7412]:
  The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG
  has an estimated oscillational period of 9.0e-03 ps, which is less than 5
  times the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

thankyou

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[gmx-users] Re: removing rotational and translational motion (holonomic contraint)

2013-03-17 Thread deplazes

Hi Tsjerk 

thanks for the patch. I have a few problems and questions

1. I get an error message when installing the patch version. This is what I
did 

tar  -xvf gromacs-3.3.1-rtc.tar

module load intel/12.1
module load intel-mkl/10.3.9
module load fftw/3.3.3
module load openmpi/1.6.3

export LDFLAGS="-L/ivec/devel/intel/12.1/fftw/3.3.3/lib"
export CPPFLAGS="-I/ivec/devel/intel/12.1/fftw/3.3.3/include"

cd /home/deplazes/gromacs-3.3.1-rtc

./configure --prefix=/home/deplazes/gromacs-3.3.1-rtc  --with-fft=fftw3
make -j4
make install

I get an error message when running make -j4, see below at the end of this
post. I used the same commands to install gromacs 3.3.3 and 3.3.1 (normal
version) and had no issues. 
It looks like a error in /src/tools/gmx_metric.c
(If I add the semi-colon on line 50 after the typedef I simply get other
errors)


After I have installed the "patched" version 

2. to"switch on" the roto-translational  constraints I set 
rototr = yes 
in the .mdp file, correct? 
according to a previous post I also need a reference structure (
ref_conf.gro). do I need to add this as an option during grompp? if so, what
command option / flag do I use? if not during grompp how do I add the
reference structure? 

3. the two examples in the paper are for a NVT and a NVE ensemble. is it ok
to use the restraints for an NPT run? I have not found any reference to it
in the paper.

thanks 
Evelyne 


---

error from "make -j4" 

gmx_metric.c(50): error: expected a ";"
  void init_matblock( int i, int j, matblock *A )
  ^

gmx_metric.c(133): error: expected a declaration
  } 
  ^

gmx_metric.c(136): error: expected a declaration
}
^

gmx_metric.c(173): error: declaration is incompatible with "char
*index(const char *, int)" (declared at line 489 of "/usr/include/string.h")
atom_id *index;
 ^

gmx_metric.c(175): error: expected a ")"
CopyRight(stderr,argv[0]);
 ^

gmx_metric.c(176): error: expected a type specifier
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
  ^

gmx_metric.c(176): error: identifier "argv" is undefined
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
^

gmx_metric.c(176): error: expected a type specifier
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
 ^

gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^

gmx_metric.c(177): error: identifier "fnm" is undefined
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
  ^

gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
  ^

gmx_metric.c(177): error: identifier "pargs" is undefined
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
   ^

gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
 ^

gmx_metric.c(177): error: identifier "desc" is undefined
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
 ^

gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
  ^

gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^

gmx_metric.c(179): error: function "ftp2fn" is not a type name
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
   ^

gmx_metric.c(179): error: expected a ")"
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
   ^

gmx_metric.c(179): error: expected a type specifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^

gmx_metric.c(179): error: identifier "fnm" is undefined
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
  ^

gmx_metric.c(179): error: declaration is incompatible with "char *title"
(declared at line 166)
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^

gmx_metric.c(179): error: expected an identifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);

RE: [gmx-users] Re: polymer duplicate atoms

2013-03-17 Thread Dallas Warren

Have you done it with polymer chain of length 1, one FRE, with the end methyl 
groups capping it off, FBG and FEN?  Does that work?

Sounds bit like the RTP entry is not set up correctly.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Monday, 18 March 2013 12:54 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
> 
> I want to construct a polymer chain of F2311 with 112 length. In my pdb
> file,
> residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)—
> ,terminate part (Fbg:the beginning of chain with methyl; Fen: the end
> of
> chain with methyl), respectively. It looks like  CH3-A-B...
> A-B-A-B-A-B...-A-B-CH3(A means -CH2-CF2- and B represent -CF2-CFCl-).
> f2311-len112.jpg
> 
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-
> tp5006328p5006394.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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[gmx-users] Re: polymer duplicate atoms

2013-03-17 Thread cqgzc

I want to construct a polymer chain of F2311 with 112 length. In my pdb file,
residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)—
,terminate part (Fbg:the beginning of chain with methyl; Fen: the end of
chain with methyl), respectively. It looks like  CH3-A-B...
A-B-A-B-A-B...-A-B-CH3(A means -CH2-CF2- and B represent -CF2-CFCl-). 
f2311-len112.jpg
  



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[gmx-users] Re: polymer duplicate atoms

2013-03-17 Thread cqgzc

I want to construct a polymer chain of F2311 with 112 length. In my pdb file,
residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)—
,terminate part (Fbg:the beginning of chain with methyl; Fen: the end of
chain with methyl), respectively. It looks like  CH3-A-B...
A-B-A-B-A-B...-A-B-CH3(A means -CH2-CF2- and B represent -CF2-CFCl-). 
f2311-len112.jpg
  



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RE: [gmx-users] Re: polymer duplicate atoms

2013-03-17 Thread Dallas Warren

That is something you will have to sort out, since you have all the files (in 
and out) and know the molecule(s) you are processing.  You have provided 
insufficient information to help without having to spend a significant amount 
of time trying to work what it all means.

If pdb2gmx is telling you that there is a strange residue in your .pdb file, 
then your formatting or numbering that you have put in there is not consistent 
with what pdb2gmx is expecting to get the "correct" output.

Have you attempted to get it work using a polymer of the shortest possible 
length?  Say two terminals?  Then added one, two etc of the middle residues?  
When starting something new and complex, you should start with something simple 
to ensure things are behaving as you expect them to, and if not it is much 
easier to work out why.  Then you make things more and more complex, until you 
are up to where you want to be.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Friday, 15 March 2013 6:20 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
> 
> Dear Dallas
> 
> Thanks for your reply. I followed the way of you said to modify the
> residue number in sequence. It generated a complete sturctural file
> (conf.gro) without deleting the duplicate atoms. However, it denoted
> another
> strange structure which contained many seperated residue
> —(CH2-CF2-CF2-CFCl)—
> It's not the polymer structure.
> f2311-new.pdb
> 
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-
> tp5006328p5006334.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] How to parameterize glucose

2013-03-17 Thread Justin Lemkul




On 3/17/13 7:32 PM, dreda wrote:

I'm trying to setup a simulation of 2 molecules of beta-D-glucose in vacuum
at 100k. I'm using the OPLS/AA force field, have a pdb file that looks good
in VMD, and have started creating the .itp file. I've described the bonds,
pairs, and angles but am having difficulty completing the parameterization:

1. If I run grompp, I get the "no default angle types" error for the angle
C1-O-H, where C1 refers to carbon-1, bonded to the O in the ring. If I
comment out just that angle in the .itp file, grompp runs without problems.
I assume this means the OPLS force field doesn't have an angle type
corresponding to that part of the molecule. Why is this and what should I do
about it?



No force field is guaranteed to accommodate any arbitrary molecule.  Most were 
designed around proteins and nucleic acids and later extended for other small 
molecules, lipids, etc.  You'll have to determine or derive suitable parameters 
for this angle if OPLS does not natively supply it.



2. I don't know how to specify dihedrals and improper dihedrals for glucose.
What's the best place to learn this?



Chapter 5 in the manual is where all elements of the topology are described.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] How to parameterize glucose

2013-03-17 Thread dreda

I'm trying to setup a simulation of 2 molecules of beta-D-glucose in vacuum
at 100k. I'm using the OPLS/AA force field, have a pdb file that looks good
in VMD, and have started creating the .itp file. I've described the bonds,
pairs, and angles but am having difficulty completing the parameterization:

1. If I run grompp, I get the "no default angle types" error for the angle
C1-O-H, where C1 refers to carbon-1, bonded to the O in the ring. If I
comment out just that angle in the .itp file, grompp runs without problems.
I assume this means the OPLS force field doesn't have an angle type
corresponding to that part of the molecule. Why is this and what should I do
about it?

2. I don't know how to specify dihedrals and improper dihedrals for glucose.
What's the best place to learn this?

Thanks,
Daniel




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Re: Fwd: Fw: Fwd: [gmx-users] position restraints

2013-03-17 Thread Justin Lemkul




On 3/17/13 6:50 AM, Shima Arasteh wrote:

Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files: 
chainA_posre.itp and chainB_posre.itp
#genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 
-n index-chain.ndx
#genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 
-n index-chain.ndx

3.Next, I included the itp files as follow in my top file:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef DPOSRE
#include "chainA_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef DPOSRE
#include "chainB_posre.itp"
#endif

4. I also added this line to my mdp file:
define = -DPOSRE

5. In addition I added these at the top of itp files for bothe restrained 
chains:
#ifdef DPOSRE
#endif

Now when I run the command :
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr

I don't get any errors.
But when I run the mdrun I don't see any position restraint terms in my log 
file.
Would you please let me know your suggestions in this about? Did I do any steps 
by mistake?



Yes, again there is a problem with the #ifdef statements.  If you use:

#ifdef DPOSRE
...
#endif

the corresponding "define" statement is -DDPOSRE.  Think of the first "D" in the 
"define" statement as "I am defining the following string to be true."  Your 
.mdp file corresponds to the use of:


#ifdef POSRE
...
#endif

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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: Fwd: Fw: Fwd: [gmx-users] position restraints

2013-03-17 Thread Shima Arasteh

Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files: 
chainA_posre.itp and chainB_posre.itp 
#genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 
-n index-chain.ndx
#genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 
-n index-chain.ndx

3.Next, I included the itp files as follow in my top file:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef DPOSRE
#include "chainA_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef DPOSRE
#include "chainB_posre.itp"
#endif

4. I also added this line to my mdp file:
define         = -DPOSRE

5. In addition I added these at the top of itp files for bothe restrained 
chains:
#ifdef DPOSRE
#endif

Now when I run the command :
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr

I don't get any errors.
But when I run the mdrun I don't see any position restraint terms in my log 
file.
Would you please let me know your suggestions in this about? Did I do any steps 
by mistake?


Thanks in advance.
Sincerely,
Shima



From: Justin Lemkul 
To: Discussion list for GROMACS users  
Sent: Saturday, March 16, 2013 4:06 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/16/13 8:34 AM, Shima Arasteh wrote:
> Thanks.
> As I understood from your emails, I need to make index groups of separate 
> chains of my protein, use the index file in order to use in genrestr command 
> and then include the specific itp files for each groups in top file?
> Do you mean this? Am I right?
> 

Yes.  Try it.

> One more thing that I need to know is that how it is possible to make an 
> index group except the options appear after running make index command?
> 

Type 'help' at the prompt or otherwise search gromacs.org and Google for 
example usage.  It is very easy to create index groups specifying subsets of 
residues or just their backbone atoms, etc.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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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