date:20110121

[gmx-users] Fwd: RMSD calculation of a specific region

2011-01-21 Thread bharat gupta

I want to calculate the rmsd of amino acid 65 to 67 of two simulated
proteins with  loop replacement in another one to find out how the position
of these 3  amino acids change due to the replacement of a loop region in
same protein ... How can I achieve it with gromacs...

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com




-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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[gmx-users] fatal error

2011-01-21 Thread ahmet yıldırım

Dear users,

Gromacs 4.5.3
pdb2gmx -f xxx.pdb -water spc
select Force Field:9
*Fatal error:*
atom C not found in buiding block 13NH2 while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


How can I fixed this error?

Thanks in advance


-- 
Ahmet YILDIRIM
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[gmx-users] charge group radii larger that rlist-rvdw

2011-01-21 Thread Kavyashree M

Dear gromacs users,

 I am using gromacs 4.5.3, OPLSAA force field, and the cut off
parameters
are as shown below:
--
---
;NEIGHBOURSEARCHING PARAMETERS
nstlist = 10 10 ; FREQUENCY WITH WHICH
NEIGHBOURLIST IS UPDATED
ns_type = grid  ; TYPE OF NEIGHBOUR SEARCH
GRID OR SIMPLE
pbc = xyz   ; DIRECTION OF PERIODIC
BOUNDARY CONDITIONS USAGE
rlist   = 1.36  ; CUT-OFF DISTANCE FOR SHORT
RANGE NEIGHBOUR LIST

;ELECTROSTATICS
coulombtype = PME   ; METHOD FOR CALCULATING
COULOMBIC INTERCATION - PME
rcoulomb= 1.36  ; CUTOFF DISTANCE FOR
ELECTROSTATIC INTERACTIONS
epsilon_r   = 1 ; RELATIVE DIELECTRIC
CONSTANT

;VAN DER WAALS
vdwtype = Switch; METHOD FOR TREATING
VANDERWAAL'S FORCES
rvdw_switch = 0.9   ; WHEN TO START SWITCHING LJ
POTENTIAL
rvdw= 1.03  ; CUTOFF DISTANCE FOR LJ OR
BUCKINGHAM INTERACTIONS

;EWALD
fourierspacing  = 0.12  ; GRID SPACING FOR FFT GRID
FOR PME
pme_order   = 4 ; INTERPOLATION ORDER FOR
PME
ewald_rtol  = 1e-5  ; RELATIVE STRENGTH OF EWALD
SHIFTED DIRECT POTENTIAL
optimize_fft= yes   ; SAVES A FEW PERCENT FOR
LONG SIMULATIONS
-

For EM (energy minimisation) I initially had used
rlist = rcolomb = 1.2;  rvdw = 1.1; rvdw_switch = 1.0
grompp gave the message:
##
Largest charge group radii for Van der Waals: 0.160, 0.157 nm
Largest charge group radii for Coulomb:   0.168, 0.167 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.317) is larger than
  rlist (1.2) - rvdw (1.1)
##
So I changed the values to: rlist = rcolomb = 1.35;  rvdw = 1.03;
rvdw_switch = 1.0
grompp message during em disappeared.

During PR (position refinement), Again the message appeared for grompp
##
Largest charge group radii for Van der Waals: 0.168, 0.156 nm
Largest charge group radii for Coulomb:   0.168, 0.164 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.324) is larger than
  rlist (1.35000) - rvdw (1.03000)
##
hence I  changed the values to: rlist = rcolomb = 1.36;  rvdw = 1.03;
rvdw_switch = 1.0
grompp message during pr disappeared.

The same message repeated for MD
###
Largest charge group radii for Van der Waals: 0.171, 0.159 nm
Largest charge group radii for Coulomb:   0.171, 0.166 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.330248) is larger than
  rlist (1.36) - rvdw (1.03)
###

My questions are:
1. Why does the charge group radii change in this way from em to pr to MD
even though I
   am using same parameters
2. What is the safest maximum value of rlist I can go up to? (is it 1.4nm
according to "The Origin
   of Layer Structure Artifacts in Simulations of Liquid Water"- JCTC, 2006,
2, 1-11 paper?)
3. What is the minimum safest rvdw distance i can take?
4. According to the manual, when using switch they have suggested that "..
neighbor search
   cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in the
above case it goes
   more than 0.3nm?

Kindly Suggest a solution.

Thanks in advance
MKS
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[gmx-users] Error in generating DPPC using grompp

2011-01-21 Thread shobana visolingam










dear all, 

i am new to gromacs and i'm trying to run the command grompp -c lipo1grobox.pdb 
-p topol.top -f em_restraints.mdp -o em_restraints.tpr.

however i got this error

Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp

ERROR 1 [file ffgmxbon_lipid.itp, line 756]:
  Invalid directive DPPC


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

Fatal error:
Syntax error - File ffgmxbon_lipid.itp, line 757
Last line read:
'[atoms]'
Invalid order for directive atoms


can i know what this error mean and how to overcome it?? thanks.

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Re: [gmx-users] Fwd: RMSD calculation of a specific region

2011-01-21 Thread Justin A. Lemkul




bharat gupta wrote:



I want to calculate the rmsd of amino acid 65 to 67 of two simulated 
proteins with  loop replacement in another one to find out how the 
position of these 3  amino acids change due to the replacement of a loop 
region in same protein ... How can I achieve it with gromacs...




Use g_rms with a suitable index group.

-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 




--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did

2011-01-21 Thread Gavin Melaugh

Dear All

Can someone please tell me how to generated the plot of mean force
having ran the pull code at several distances using constraints?

Gavin
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[gmx-users] Pull code

2011-01-21 Thread Gavin Melaugh

Dear All

Sorry wrong subject title in previous post. Can someone please tell me how to 
generated the plot of mean force
having ran the pull code at several distances using constraints?

Gavin

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Re: [gmx-users] charge group radii larger that rlist-rvdw

2011-01-21 Thread Justin A. Lemkul




Kavyashree M wrote:

Dear gromacs users,

 I am using gromacs 4.5.3, OPLSAA force field, and the cut off 
parameters

are as shown below:
-
;NEIGHBOURSEARCHING PARAMETERS
nstlist = 10 10 ; FREQUENCY WITH WHICH 
NEIGHBOURLIST IS UPDATED
ns_type = grid  ; TYPE OF NEIGHBOUR 
SEARCH GRID OR SIMPLE
pbc = xyz   ; DIRECTION OF PERIODIC 
BOUNDARY CONDITIONS USAGE
rlist   = 1.36  ; CUT-OFF DISTANCE FOR 
SHORT RANGE NEIGHBOUR LIST


;ELECTROSTATICS
coulombtype = PME   ; METHOD FOR CALCULATING 
COULOMBIC INTERCATION - PME
rcoulomb= 1.36  ; CUTOFF DISTANCE FOR 
ELECTROSTATIC INTERACTIONS
epsilon_r   = 1 ; RELATIVE DIELECTRIC 
CONSTANT


;VAN DER WAALS
vdwtype = Switch; METHOD FOR TREATING 
VANDERWAAL'S FORCES
rvdw_switch = 0.9   ; WHEN TO START 
SWITCHING LJ POTENTIAL
rvdw= 1.03  ; CUTOFF DISTANCE FOR LJ 
OR BUCKINGHAM INTERACTIONS


;EWALD
fourierspacing  = 0.12  ; GRID SPACING FOR FFT 
GRID FOR PME
pme_order   = 4 ; INTERPOLATION ORDER 
FOR PME
ewald_rtol  = 1e-5  ; RELATIVE STRENGTH OF 
EWALD SHIFTED DIRECT POTENTIAL
optimize_fft= yes   ; SAVES A FEW PERCENT 
FOR LONG SIMULATIONS

-

For EM (energy minimisation) I initially had used
rlist = rcolomb = 1.2;  rvdw = 1.1; rvdw_switch = 1.0
grompp gave the message:
##
Largest charge group radii for Van der Waals: 0.160, 0.157 nm
Largest charge group radii for Coulomb:   0.168, 0.167 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.317) is larger than
  rlist (1.2) - rvdw (1.1)
##
So I changed the values to: rlist = rcolomb = 1.35;  rvdw = 1.03; 
rvdw_switch = 1.0

grompp message during em disappeared.

During PR (position refinement), Again the message appeared for grompp
##
Largest charge group radii for Van der Waals: 0.168, 0.156 nm
Largest charge group radii for Coulomb:   0.168, 0.164 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.324) is larger than
  rlist (1.35000) - rvdw (1.03000)
##
hence I  changed the values to: rlist = rcolomb = 1.36;  rvdw = 1.03; 
rvdw_switch = 1.0

grompp message during pr disappeared.

The same message repeated for MD
###
Largest charge group radii for Van der Waals: 0.171, 0.159 nm
Largest charge group radii for Coulomb:   0.171, 0.166 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.330248) is larger than
  rlist (1.36) - rvdw (1.03)
###

My questions are:
1. Why does the charge group radii change in this way from em to pr to 
MD even though I

   am using same parameters


Because EM changes coordinates, so the configurations of those charge groups 
probably changed.


2. What is the safest maximum value of rlist I can go up to? (is it 
1.4nm according to "The Origin
   of Layer Structure Artifacts in Simulations of Liquid Water"- JCTC, 
2006, 2, 1-11 paper?)

3. What is the minimum safest rvdw distance i can take?


For #2 and #3, you should use settings that are recommended for the OPLS force 
field.  Refer to the original literature for the force field.


4. According to the manual, when using switch they have suggested that 
".. neighbor search
   cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in 
the above case it goes

   more than 0.3nm?



Usually over 0.3 nm is not necessary, but it seems in your case that you have 
some relatively large charge groups.  This may or may not indicate something is 
wrong with your topology.


The ad hoc changes you have made to the cutoffs to make a grompp message go away 
are probably not suitable.  Refer to the OPLS papers for proper settings.


-Justin


Thanks in advance
MKS



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] fatal error

2011-01-21 Thread Justin A. Lemkul




ahmet yıldırım wrote:

Dear users,

Gromacs 4.5.3
pdb2gmx -f xxx.pdb -water spc
select Force Field:9
*Fatal error:*
atom C not found in buiding block 13NH2 while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


How can I fixed this error?



You have a carbon atom in a residue that should only contain NH2.  Refer to the 
.rtp file for what is expected, then make a suitable structure that conforms to 
those requirements.


This has been asked and answered hundreds of times, so please make use of the 
mailing list search.  You would have gotten your answer in minutes rather than 
hours.


-Justin


Thanks in advance


--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Error in generating DPPC using grompp

2011-01-21 Thread Justin A. Lemkul




shobana visolingam wrote:






dear all,

i am new to gromacs and i'm trying to run the command grompp -c 
lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr.


however i got this error

*Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp

ERROR 1 [file ffgmxbon_lipid.itp, line 756]:
  Invalid directive DPPC


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

Fatal error:
Syntax error - File ffgmxbon_lipid.itp, line 757
Last line read:
'[atoms]'
Invalid order for directive atoms*


can i know what this error mean and how to overcome it?? thanks.



You have serious errors in your topology.  Without seeing it, there's nothing 
else anyone can really suggest except for having a thorough read through Chapter 
5.  The topology must follow a specific order, which you likely have not 
followed.  A simple DPPC topology is available as part of my membrane protein 
tutorial:


http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did

2011-01-21 Thread Justin A. Lemkul




Gavin Melaugh wrote:

Dear All

Can someone please tell me how to generated the plot of mean force
having ran the pull code at several distances using constraints?



Would the mean force not simply be the average value found in pullf.xvg?

-Justin


Gavin


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] DSPC all atom .itp file

2011-01-21 Thread Anirban Ghosh

Hi ALL,

Can anyone please send me an all-atom DSPC .itp file at *
reach.anirban.gh...@gmail.com *or* anirba...@gmail.com*
*
*
Thanks a lot.


-Anirban
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[gmx-users] OPLS implicit solvent problems

2011-01-21 Thread francesca . stanzione




  Hello,

  I try to perform an implicit solvent simulation with Gromacs 4.5.3.  
version. I have a system corresponding to 6 peptides generated by  
Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA  
and i put the N-and C- termini as NH2 and COOH. My topology file is  
correct, and is all systems are included.


  ; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp" ---> in this .itp file is  
included gbsa.itp


; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_E.itp"
#include "topol_Protein_chain_F.itp"

; Include water topology
#include "./oplsaa.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1   1000   1000   1000
#endif
 
; Include topology for ions
#include "./oplsaa.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound    #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
-

  When I start my simulations (md_start.mdp) in implicit solvent, i  
have this fatal error:


  GB parameter(s) missing or negative for atom type 'opls_912B'

GB parameter(s) missing or negative for atom type 'opls_267'

GB parameter(s) missing or negative for atom type 'opls_269'

GB parameter(s) missing or negative for atom type 'opls_268'

GB parameter(s) missing or negative for atom type 'opls_270'

  Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1123

Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the  
forcefield is missing parameters for 5 atomtypes or they might be  
negative.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors.

  

  Controlling these atoms they corresponding to:

  opls_912B= the  CA of N-terminal residue

  opls_267= Co in COOH

  opls_268= Oh in COOH

  opls_269= Oc in COOH neutral

  opls_270= H in COOH

  

  in the file gbsa.itp in opls.ff directory these atoms missing. Now,  
have I done something wrong? If is all ok, is it possible to create  
these missing atoms in the gbsa.itp file?


  thanx,

  francesca stanzione
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Re: [gmx-users] OPLS implicit solvent problems

2011-01-21 Thread Per Larsson

Hi!

Thanks for pointing this out.
It is unfortunate that they are missing from the gbsa.itp-file. I will add 
them, but I do not have time today.
If you want to get going, you can add them yourself. 
The gb-parameters are essentially based on atom hybridization, so for each 
missing atom you find another that has the same (sp, sp2,sp3) hybridization, 
and add it to the gbsa.itp-file.

Cheers
/Per

21 jan 2011 kl. 13.51 skrev francesca.stanzi...@unina.it:

> Hello,
> 
> I try to perform an implicit solvent simulation with Gromacs 4.5.3. version. 
> I have a system corresponding to 6 peptides generated by Pymol with 
> simmetrical cell, so I have a single PDB. I used OPLS-AA and i put the N-and 
> C- termini as NH2 and COOH. My topology file is correct, and is all systems 
> are included.
> 
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp" ---> in this .itp file is included 
> gbsa.itp
> 
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
> 
> ; Include water topology
> #include "./oplsaa.ff/tip3p.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>  
> ; Include topology for ions
> #include "./oplsaa.ff/ions.itp"
> 
> [ system ]
> ; Name
> Protein
> 
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> Protein_chain_B 1
> Protein_chain_C 1
> Protein_chain_D 1
> Protein_chain_E 1
> Protein_chain_F 1
> -
> 
> When I start my simulations (md_start.mdp) in implicit solvent, i have this 
> fatal error:
> 
> GB parameter(s) missing or negative for atom type 'opls_912B'
> 
> GB parameter(s) missing or negative for atom type 'opls_267'
> 
> GB parameter(s) missing or negative for atom type 'opls_269'
> 
> GB parameter(s) missing or negative for atom type 'opls_268'
> 
> GB parameter(s) missing or negative for atom type 'opls_270'
> 
> Program grompp, VERSION 4.5.3
> Source code file: grompp.c, line: 1123
> 
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the 
> forcefield is missing parameters for 5 atomtypes or they might be negative.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors.
> 
> 
> 
> Controlling these atoms they corresponding to:
> 
> opls_912B= the  CA of N-terminal residue
> 
> opls_267= Co in COOH
> 
> opls_268= Oh in COOH
> 
> opls_269= Oc in COOH neutral
> 
> opls_270= H in COOH
> 
> 
> 
> in the file gbsa.itp in opls.ff directory these atoms missing. Now, have I 
> done something wrong? If is all ok, is it possible to create these missing 
> atoms in the gbsa.itp file?
> 
> thanx,
> 
> francesca stanzione
> 
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[gmx-users] (no subject)

2011-01-21 Thread francesca . stanzione




  Hi Pers,

  thank you for reply. I'm trying to add these missing atoms with  
your guideline, but I don't know if all parameters that I'm going to  
add are corrects. When you have a time, can you add these missing  
atoms in the program or can you help me to create a correct  
substitution of these atoms? Because I can try  to add the parameters  
in the five coloumns present but I should know if these values are  
right.


  thanks,

  francesca
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[gmx-users] CG to FG transformation error

2011-01-21 Thread Anirban Ghosh

Hi,

I am trying to convert a coarse grained protein to a full atom model after
CGMD. I am using the modified gromacs_reverse code available from MARTINI
site. I am using the following command:

g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro

But in the output full.gro all the atoms are having coordinate values as
"0.00".

My pro_cg.top file looks like:

#define _FF_GROMOS96
#define _FF_GROMOS42A2
;#define _FF_GROMACS
;#define _FF_GROMACS1

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1   1   yes 0.125   0.5


#include "ffG43a2nb.itp"
#include "ffG43a2bon.itp"


Is this correct? where I am going wrong? I think the problem is with
pro_cg.top file only.

Any suggestion is welcome.


Thanks,


-Anirban
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Re: [gmx-users] Problem with using topolbuild1_3.tgz

2011-01-21 Thread Bruce D. Ray

On Thu, January 20, 2011 at 6:41PM, Sweta Iyer  wrote:
> Hi, I am trying to generate topology files for a set of lipids with the
> help of topolbuild1_3.tgz package found at the other software page of
> GROMACS website.
> 
> I downloaded and installed all files and tried running the program with a
> MOL2 file with charges in it. However, it shows an error message as
> follows:
> 
> Fatal error.
> Source code file: readmol2.c, line: 758
> Atom 1 (C) has 3 connections when allowed 0
> 
> I am not sure how to get over this problem! Wonder what will fix this
> error and get the program running!

A major requirement of topolbuild is that the mol2 file use correct atom
types as defined by Tripos, whose file format mol2 is, and as used in Sybyl.
The error message suggests that you have not specified correct Tripos Sybyl
atom types.  There may be other problems in your mol2 file as well.
Correct the atom types and check that the file is otherwise syntactically
correct and it should work.

However, I believe that lipid topology files for gromacs are already available
for download.

I hope that helps.

-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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Re: [gmx-users] CG to FG transformation error

2011-01-21 Thread Martti Louhivuori


On 21 Jan 2011, at 14:47, Anirban Ghosh wrote:
I am trying to convert a coarse grained protein to a full atom model  
after CGMD. I am using the modified gromacs_reverse code available  
from MARTINI site. I am using the following command:


g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o  
full.gro


But in the output full.gro all the atoms are having coordinate  
values as "0.00".


My pro_cg.top file looks like:

#define _FF_GROMOS96
#define _FF_GROMOS42A2
;#define _FF_GROMACS
;#define _FF_GROMACS1

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1   1   yes 0.125   0.5


#include "ffG43a2nb.itp"
#include "ffG43a2bon.itp"


Is this correct? where I am going wrong? I think the problem is with  
pro_cg.top file only.


No. The problem is indeed your pro_cg.top. It should be a *CG  
topology* (like what you've used for the CG simulations), not an  
*atomistic FF*.


-martti-
--
Post-doctoral research fellow
Moleculaire Dynamica
University of Groningen
Nijenborgh 4, 9747AG Groningen, the Netherlands
tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398

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Re: [gmx-users] charge group radii larger that rlist-rvdw

2011-01-21 Thread Kavyashree M

Sir,

   What exactly can be wrong with the topology? As I tried with
different PDBs of same structure at higher resolutions too, I am getting
almost similar charge group radii, so can you kindly elaborate about
what can go wrong in the topology to get such values?

Thanks
MKS

On Fri, Jan 21, 2011 at 5:20 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>
>> I am using gromacs 4.5.3, OPLSAA force field, and the cut off
>> parameters
>> are as shown below:
>>
>> -
>> ;NEIGHBOURSEARCHING PARAMETERS
>> nstlist = 10 10 ; FREQUENCY WITH WHICH
>> NEIGHBOURLIST IS UPDATED
>> ns_type = grid  ; TYPE OF NEIGHBOUR SEARCH
>> GRID OR SIMPLE
>> pbc = xyz   ; DIRECTION OF PERIODIC
>> BOUNDARY CONDITIONS USAGE
>> rlist   = 1.36  ; CUT-OFF DISTANCE FOR
>> SHORT RANGE NEIGHBOUR LIST
>>
>> ;ELECTROSTATICS
>> coulombtype = PME   ; METHOD FOR CALCULATING
>> COULOMBIC INTERCATION - PME
>> rcoulomb= 1.36  ; CUTOFF DISTANCE FOR
>> ELECTROSTATIC INTERACTIONS
>> epsilon_r   = 1 ; RELATIVE DIELECTRIC
>> CONSTANT
>>
>> ;VAN DER WAALS
>> vdwtype = Switch; METHOD FOR TREATING
>> VANDERWAAL'S FORCES
>> rvdw_switch = 0.9   ; WHEN TO START SWITCHING
>> LJ POTENTIAL
>> rvdw= 1.03  ; CUTOFF DISTANCE FOR LJ
>> OR BUCKINGHAM INTERACTIONS
>>
>> ;EWALD
>> fourierspacing  = 0.12  ; GRID SPACING FOR FFT
>> GRID FOR PME
>> pme_order   = 4 ; INTERPOLATION ORDER FOR
>> PME
>> ewald_rtol  = 1e-5  ; RELATIVE STRENGTH OF
>> EWALD SHIFTED DIRECT POTENTIAL
>> optimize_fft= yes   ; SAVES A FEW PERCENT FOR
>> LONG SIMULATIONS
>>
>> -
>>
>> For EM (energy minimisation) I initially had used
>> rlist = rcolomb = 1.2;  rvdw = 1.1; rvdw_switch = 1.0
>> grompp gave the message:
>> ##
>> Largest charge group radii for Van der Waals: 0.160, 0.157 nm
>> Largest charge group radii for Coulomb:   0.168, 0.167 nm
>>
>> NOTE 1 [file md.mdp]:
>>  The sum of the two largest charge group radii (0.317) is larger than
>>  rlist (1.2) - rvdw (1.1)
>> ##
>> So I changed the values to: rlist = rcolomb = 1.35;  rvdw = 1.03;
>> rvdw_switch = 1.0
>> grompp message during em disappeared.
>>
>> During PR (position refinement), Again the message appeared for grompp
>> ##
>> Largest charge group radii for Van der Waals: 0.168, 0.156 nm
>> Largest charge group radii for Coulomb:   0.168, 0.164 nm
>>
>> NOTE 1 [file md.mdp]:
>>  The sum of the two largest charge group radii (0.324) is larger than
>>  rlist (1.35000) - rvdw (1.03000)
>> ##
>> hence I  changed the values to: rlist = rcolomb = 1.36;  rvdw = 1.03;
>> rvdw_switch = 1.0
>> grompp message during pr disappeared.
>>
>> The same message repeated for MD
>> ###
>> Largest charge group radii for Van der Waals: 0.171, 0.159 nm
>> Largest charge group radii for Coulomb:   0.171, 0.166 nm
>>
>> NOTE 1 [file md.mdp]:
>>  The sum of the two largest charge group radii (0.330248) is larger than
>>  rlist (1.36) - rvdw (1.03)
>> ###
>>
>> My questions are:
>> 1. Why does the charge group radii change in this way from em to pr to MD
>> even though I
>>   am using same parameters
>>
>
> Because EM changes coordinates, so the configurations of those charge
> groups probably changed.
>
>
>  2. What is the safest maximum value of rlist I can go up to? (is it 1.4nm
>> according to "The Origin
>>   of Layer Structure Artifacts in Simulations of Liquid Water"- JCTC,
>> 2006, 2, 1-11 paper?)
>> 3. What is the minimum safest rvdw distance i can take?
>>
>
> For #2 and #3, you should use settings that are recommended for the OPLS
> force field.  Refer to the original literature for the force field.
>
>
>  4. According to the manual, when using switch they have suggested that "..
>> neighbor search
>>   cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in
>> the above case it goes
>>   more than 0.3nm?
>>
>>
> Usually over 0.3 nm is not necessary, but it seems in your case that you
> have some relatively large charge groups.  This may or may not indicate
> something is wrong with your topology.
>
> The ad hoc changes you have made to the cutoffs to make a grompp message go
> away are probably not suitable.  Refer to the OPLS papers for proper
> settings.
>
> -Justin
>
>  Thanks in advance
>> MKS
>>
>>
> --
> 
>
> Justin A. L

Re: [gmx-users] charge group radii larger that rlist-rvdw

2011-01-21 Thread Justin A. Lemkul




Kavyashree M wrote:

Sir,

   What exactly can be wrong with the topology? As I tried with


I don't know, what's in your system?  Was the topology created entirely by 
pdb2gmx, or have you introduced some other molecules that you've parameterized?



different PDBs of same structure at higher resolutions too, I am getting
almost similar charge group radii, so can you kindly elaborate about
what can go wrong in the topology to get such values?



Large charge groups indicate that a fair number of atoms have been included in 
the same charge group.  Usually only two or three atoms are in a charge group, 
rendering them fairly small.  With PME, the effects may not be that large, i.e. 
http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html, but it's 
still worth investigating what your largest charge group is that's causing this 
problem.  If the topology is sound and is based entirely upon standard force 
field files, it may suffice to simply increase rlist to 1.4 nm, leaving all the 
other cutoffs at 1.0, which I believe is standard for OPLS (but don't just take 
my word for it).


-Justin


Thanks
MKS

On Fri, Jan 21, 2011 at 5:20 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Dear gromacs users,

I am using gromacs 4.5.3, OPLSAA force field, and the cut
off parameters
are as shown below:

-
;NEIGHBOURSEARCHING PARAMETERS
nstlist = 10 10 ; FREQUENCY WITH
WHICH NEIGHBOURLIST IS UPDATED
ns_type = grid  ; TYPE OF
NEIGHBOUR SEARCH GRID OR SIMPLE
pbc = xyz   ; DIRECTION OF
PERIODIC BOUNDARY CONDITIONS USAGE
rlist   = 1.36  ; CUT-OFF
DISTANCE FOR SHORT RANGE NEIGHBOUR LIST

;ELECTROSTATICS
coulombtype = PME   ; METHOD FOR
CALCULATING COULOMBIC INTERCATION - PME
rcoulomb= 1.36  ; CUTOFF
DISTANCE FOR ELECTROSTATIC INTERACTIONS
epsilon_r   = 1 ; RELATIVE
DIELECTRIC CONSTANT

;VAN DER WAALS
vdwtype = Switch; METHOD FOR
TREATING VANDERWAAL'S FORCES
rvdw_switch = 0.9   ; WHEN TO START
SWITCHING LJ POTENTIAL
rvdw= 1.03  ; CUTOFF
DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS

;EWALD
fourierspacing  = 0.12  ; GRID SPACING
FOR FFT GRID FOR PME
pme_order   = 4 ; INTERPOLATION
ORDER FOR PME
ewald_rtol  = 1e-5  ; RELATIVE
STRENGTH OF EWALD SHIFTED DIRECT POTENTIAL
optimize_fft= yes   ; SAVES A FEW
PERCENT FOR LONG SIMULATIONS

-

For EM (energy minimisation) I initially had used
rlist = rcolomb = 1.2;  rvdw = 1.1; rvdw_switch = 1.0
grompp gave the message:
##
Largest charge group radii for Van der Waals: 0.160, 0.157 nm
Largest charge group radii for Coulomb:   0.168, 0.167 nm

NOTE 1 [file md.mdp]:
 The sum of the two largest charge group radii (0.317) is larger
than
 rlist (1.2) - rvdw (1.1)
##
So I changed the values to: rlist = rcolomb = 1.35;  rvdw =
1.03; rvdw_switch = 1.0
grompp message during em disappeared.

During PR (position refinement), Again the message appeared for
grompp
##
Largest charge group radii for Van der Waals: 0.168, 0.156 nm
Largest charge group radii for Coulomb:   0.168, 0.164 nm

NOTE 1 [file md.mdp]:
 The sum of the two largest charge group radii (0.324) is larger
than
 rlist (1.35000) - rvdw (1.03000)
##
hence I  changed the values to: rlist = rcolomb = 1.36;  rvdw =
1.03; rvdw_switch = 1.0
grompp message during pr disappeared.

The same message repeated for MD
###
Largest charge group radii for Van der Waals: 0.171, 0.159 nm
Largest charge group radii for Coulomb:   0.171, 0.166 nm

NOTE 1 [file md.mdp]:
 The sum of the two largest charge group radii (0.330248) is
larger than
 rlist (1.36) - rvdw (1.03)
###

My questions are:
1. Why does the charge group radii change in this way from em to
pr to MD ev

[gmx-users] RNA with small molecule

2011-01-21 Thread Muslum Ilgu

Hi all,

I am trying to simulate RNA with a small molecule. However, I could not find
any parameter file described for RNA and small molecule. If anyone knows and
shares with me, it is appreciated.

Thanks a lot
Muslum
-- 
Muslum ILGU
PhD Candidate, Nilsen-Hamilton Laboratory
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
3228 Mol. Bio. Bldg
Ames, IA 50011
office (515) 294-7305

" It´s not a shame not to know; what is bad is not asking ".
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Re: [gmx-users] RNA with small molecule

2011-01-21 Thread Justin A. Lemkul




Muslum Ilgu wrote:

Hi all,

I am trying to simulate RNA with a small molecule. However, I could not 
find any parameter file described for RNA and small molecule. If anyone 
knows and shares with me, it is appreciated. 



You haven't said what force field you'd like to use, which is an important 
choice.  Don't pick a force field based on whether or not it contains your 
molecules by default.  Most of them won't contain everything, anyway, in which 
case you have to derive the parameters yourself:


http://www.gromacs.org/Documentation/How-tos/Parameterization

Since you haven't even said what the small molecule is (ethanol? a drug? a 
lipid?) then no one here will be able to do much to help you.


-Justin


Thanks a lot
Muslum
--
Muslum ILGU
PhD Candidate, Nilsen-Hamilton Laboratory
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
3228 Mol. Bio. Bldg
Ames, IA 50011
office (515) 294-7305

" It´s not a shame not to know; what is bad is not asking ".



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] RNA with small molecule

2011-01-21 Thread Muslum Ilgu

Hi again,
I am sorry I fotgot to mention that I will simulate a drug (an antibiotic)
with 23mer RNA molecule. I am potentially using GROMOS as a force field to.

Thanks

On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul  wrote:

>
>
> Muslum Ilgu wrote:
>
>> Hi all,
>>
>> I am trying to simulate RNA with a small molecule. However, I could not
>> find any parameter file described for RNA and small molecule. If anyone
>> knows and shares with me, it is appreciated.
>>
>
> You haven't said what force field you'd like to use, which is an important
> choice.  Don't pick a force field based on whether or not it contains your
> molecules by default.  Most of them won't contain everything, anyway, in
> which case you have to derive the parameters yourself:
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> Since you haven't even said what the small molecule is (ethanol? a drug? a
> lipid?) then no one here will be able to do much to help you.
>
> -Justin
>
>  Thanks a lot
>> Muslum
>> --
>> Muslum ILGU
>> PhD Candidate, Nilsen-Hamilton Laboratory
>> Department of Biochemistry, Biophysics and Molecular Biology
>> Iowa State University
>> 3228 Mol. Bio. Bldg
>> Ames, IA 50011
>> office (515) 294-7305
>>
>> " It愀 not a shame not to know; what is bad is not asking ".
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] RNA with small molecule

2011-01-21 Thread Justin A. Lemkul




Muslum Ilgu wrote:

Hi again,
I am sorry I fotgot to mention that I will simulate a drug (an 
antibiotic) with 23mer RNA molecule. I am potentially using GROMOS as a 
force field to.




GROMOS is a relatively poor choice for simulations involving nucleic acids. 
CHARMM or AMBER would be a better choice.  The parameterization advice still 
applies.  There are no easy answers.  Parameterization may take weeks or months 
and is considered an advanced topic.  Not to dissuade you from trying, but be 
aware that you're in for a long road no matter what you do.


-Justin

Thanks 

On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul > wrote:




Muslum Ilgu wrote:

Hi all,

I am trying to simulate RNA with a small molecule. However, I
could not find any parameter file described for RNA and small
molecule. If anyone knows and shares with me, it is appreciated.


You haven't said what force field you'd like to use, which is an
important choice.  Don't pick a force field based on whether or not
it contains your molecules by default.  Most of them won't contain
everything, anyway, in which case you have to derive the parameters
yourself:

http://www.gromacs.org/Documentation/How-tos/Parameterization

Since you haven't even said what the small molecule is (ethanol? a
drug? a lipid?) then no one here will be able to do much to help you.

-Justin

Thanks a lot
Muslum
-- 
Muslum ILGU

PhD Candidate, Nilsen-Hamilton Laboratory
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
3228 Mol. Bio. Bldg
Ames, IA 50011
office (515) 294-7305

" It愀 not a shame not to know; what is bad is not asking ".


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
MILES-IGERT Trainee
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] fatal error

2011-01-21 Thread ahmet yıldırım

I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as
far as I understand from mailing list. I am using 43a1 forcefield. I do not
understand what kind of changes should I do.

*the aminoacids.rtp file:*
[ ACE ]
 [ atoms ]
CA   CH3   0.000 0
 C C   0.380 1
 O O  -0.380 1
 [ bonds ]
 CCA   gb_26
 C O   gb_4
 C+N   gb_9
 [ angles ]
   CA C Oga_30
   CA C+Nga_18
O C+Nga_32
 [ impropers ]
CCA+N Ogi_1

[ NH2 ]
 [ atoms ]
 NNT   -0.830
 H1H   0.4150
 H2H   0.415   0
 [ bonds ]
  NH1  gb_2
  NH2  gb_2
 -CN   gb_8
 [ angles ]
 -O -C N  ga_32
 -CA -C N ga_18
 -C N H1  ga_22
 -C N H2  ga_22
 H1 N H2  ga_23
 [ dihedrals ]
-CA -C N H1 gd_4
 [ impropers ]
-C -O N -CA gi_1
 N  H1 H2  -C gi_1

[ ALA ]
 [ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH3 0.0 1
C C   0.380 2
O O  -0.380 2
 [ bonds ]
N Hgb_2
NCAgb_20
   CA Cgb_26
C Ogb_4
C+Ngb_9
   CACBgb_26

2011/1/21 Justin A. Lemkul 

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> Gromacs 4.5.3
>> pdb2gmx -f xxx.pdb -water spc
>> select Force Field:9
>> *Fatal error:*
>> atom C not found in buiding block 13NH2 while combining tdb and rtp
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> How can I fixed this error?
>>
>>
> You have a carbon atom in a residue that should only contain NH2.  Refer to
> the .rtp file for what is expected, then make a suitable structure that
> conforms to those requirements.
>
> This has been asked and answered hundreds of times, so please make use of
> the mailing list search.  You would have gotten your answer in minutes
> rather than hours.
>
> -Justin
>
>
>  Thanks in advance
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
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Re: [gmx-users] fatal error

2011-01-21 Thread Justin A. Lemkul




ahmet yıldırım wrote:
I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder 
as far as I understand from mailing list. I am using 43a1 forcefield. I 
do not understand what kind of changes should I do.




You do not need to modify the .rtp file, you need to modify your coordinate 
file, as I said before.  The fatal error indicates that you have included a C 
atom in an NH2 residue, which is just a neutral amine and contains no carbon, as 
should be clear from the .rtp file.


-Justin


*the aminoacids.rtp file:*
[ ACE ]
 [ atoms ]
CA   CH3   0.000 0
 C C   0.380 1
 O O  -0.380 1
 [ bonds ]
 CCA   gb_26
 C O   gb_4
 C+N   gb_9
 [ angles ]
   CA C Oga_30
   CA C+Nga_18
O C+Nga_32
 [ impropers ]
CCA+N Ogi_1

[ NH2 ]
 [ atoms ]
 NNT   -0.830
 H1H   0.4150
 H2H   0.415   0
 [ bonds ]
  NH1  gb_2
  NH2  gb_2  
 -CN   gb_8

 [ angles ]
 -O -C N  ga_32
 -CA -C N ga_18
 -C N H1  ga_22
 -C N H2  ga_22
 H1 N H2  ga_23
 [ dihedrals ]
-CA -C N H1 gd_4
 [ impropers ]
-C -O N -CA gi_1
 N  H1 H2  -C gi_1

[ ALA ]
 [ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH3 0.0 1
C C   0.380 2
O O  -0.380 2
 [ bonds ]
N Hgb_2   
NCAgb_20  
   CA Cgb_26  
C Ogb_4   
C+Ngb_9   
   CACBgb_26  


2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>



ahmet yıldırım wrote:

Dear users,

Gromacs 4.5.3
pdb2gmx -f xxx.pdb -water spc
select Force Field:9
*Fatal error:*
atom C not found in buiding block 13NH2 while combining tdb and rtp
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors


How can I fixed this error?


You have a carbon atom in a residue that should only contain NH2.
 Refer to the .rtp file for what is expected, then make a suitable
structure that conforms to those requirements.

This has been asked and answered hundreds of times, so please make
use of the mailing list search.  You would have gotten your answer
in minutes rather than hours.

-Justin


Thanks in advance


-- 
Ahmet YILDIRIM



-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Please search the archive at
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--
Ahmet YILDIRIM


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] fatal error

2011-01-21 Thread ahmet yıldırım

Dear justin,

I looked at the pdb file. No NH2 reside contains carbon atom.

What should I do?

22 Ocak 2011 00:18 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as
>> far as I understand from mailing list. I am using 43a1 forcefield. I do not
>> understand what kind of changes should I do.
>>
>>
> You do not need to modify the .rtp file, you need to modify your coordinate
> file, as I said before.  The fatal error indicates that you have included a
> C atom in an NH2 residue, which is just a neutral amine and contains no
> carbon, as should be clear from the .rtp file.
>
> -Justin
>
>  *the aminoacids.rtp file:*
>>
>> [ ACE ]
>>  [ atoms ]
>>CA   CH3   0.000 0
>> C C   0.380 1
>> O O  -0.380 1
>>  [ bonds ]
>> CCA   gb_26
>> C O   gb_4
>> C+N   gb_9
>>  [ angles ]
>>   CA C Oga_30
>>   CA C+Nga_18
>>O C+Nga_32
>>  [ impropers ]
>>CCA+N Ogi_1
>>
>> [ NH2 ]
>>  [ atoms ]
>> NNT   -0.830
>> H1H   0.4150
>> H2H   0.415   0
>>  [ bonds ]
>>  NH1  gb_2
>>  NH2  gb_2   -CN   gb_8
>>  [ angles ]
>> -O -C N  ga_32
>> -CA -C N ga_18
>> -C N H1  ga_22
>> -C N H2  ga_22
>> H1 N H2  ga_23
>>  [ dihedrals ]
>>-CA -C N H1 gd_4
>>  [ impropers ]
>>-C -O N -CA gi_1
>> N  H1 H2  -C gi_1
>>
>> [ ALA ]
>>  [ atoms ]
>>N N-0.28000 0
>>H H 0.28000 0
>>   CA   CH1 0.0 1
>>   CB   CH3 0.0 1
>>C C   0.380 2
>>O O  -0.380 2
>>  [ bonds ]
>>N Hgb_2   NCAgb_20 CA Cgb_26  C
>> Ogb_4   C+Ngb_9  CACBgb_26
>> 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>ahmet yıldırım wrote:
>>
>>Dear users,
>>
>>Gromacs 4.5.3
>>pdb2gmx -f xxx.pdb -water spc
>>select Force Field:9
>>*Fatal error:*
>>atom C not found in buiding block 13NH2 while combining tdb and rtp
>>For more information and tips for troubleshooting, please check
>>the GROMACS
>>website at http://www.gromacs.org/Documentation/Errors
>>
>>
>>How can I fixed this error?
>>
>>
>>You have a carbon atom in a residue that should only contain NH2.
>> Refer to the .rtp file for what is expected, then make a suitable
>>structure that conforms to those requirements.
>>
>>This has been asked and answered hundreds of times, so please make
>>use of the mailing list search.  You would have gotten your answer
>>in minutes rather than hours.
>>
>>-Justin
>>
>>
>>Thanks in advance
>>
>>
>>-- Ahmet YILDIRIM
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] fatal error

2011-01-21 Thread Justin A. Lemkul

ahmet yıldırım wrote:

Dear justin,

I looked at the pdb file. No NH2 reside contains carbon atom.

What should I do?

In this case, you need to manually specify termini.  Choose "None" to allow your 
capping groups to be built properly.

-Justin

22 Ocak 2011 00:18 tarihinde Justin A. Lemkul > yazdı:

ahmet yıldırım wrote:

I think I need to edit the aminoacids.rtp file in gromos43a1.ff
folder as far as I understand from mailing list. I am using 43a1
forcefield. I do not understand what kind of changes should I do.

You do not need to modify the .rtp file, you need to modify your
coordinate file, as I said before.  The fatal error indicates that
you have included a C atom in an NH2 residue, which is just a
neutral amine and contains no carbon, as should be clear from the
.rtp file.

-Justin

*the aminoacids.rtp file:*

[ ACE ]
 [ atoms ]
   CA   CH3   0.000 0
C C   0.380 1
O O  -0.380 1
 [ bonds ]
CCA   gb_26
C O   gb_4
C+N   gb_9
 [ angles ]
  CA C Oga_30
  CA C+Nga_18
   O C+Nga_32
 [ impropers ]
   CCA+N Ogi_1

[ NH2 ]
 [ atoms ]
NNT   -0.830
H1H   0.4150
H2H   0.415   0
 [ bonds ]
 NH1  gb_2
 NH2  gb_2   -CN   gb_8
 [ angles ]
-O -C N  ga_32
-CA -C N ga_18
-C N H1  ga_22
-C N H2  ga_22
H1 N H2  ga_23
 [ dihedrals ]
   -CA -C N H1 gd_4
 [ impropers ]
   -C -O N -CA gi_1
N  H1 H2  -C gi_1

[ ALA ]
 [ atoms ]
   N N-0.28000 0
   H H 0.28000 0
  CA   CH1 0.0 1
  CB   CH3 0.0 1
   C C   0.380 2
   O O  -0.380 2
 [ bonds ]
   N Hgb_2   NCAgb_20 CA Cgb_26
 C Ogb_4   C+Ngb_9  CACBgb_26  
2011/1/21 Justin A. Lemkul 
 >>

   ahmet yıldırım wrote:

   Dear users,

   Gromacs 4.5.3
   pdb2gmx -f xxx.pdb -water spc
   select Force Field:9
   *Fatal error:*
   atom C not found in buiding block 13NH2 while combining
tdb and rtp
   For more information and tips for troubleshooting, please
check
   the GROMACS
   website at http://www.gromacs.org/Documentation/Errors

   How can I fixed this error?

   You have a carbon atom in a residue that should only contain NH2.
Refer to the .rtp file for what is expected, then make a
suitable
   structure that conforms to those requirements.

   This has been asked and answered hundreds of times, so please
make
   use of the mailing list search.  You would have gotten your
answer
   in minutes rather than hours.

   -Justin

   Thanks in advance

   -- Ahmet YILDIRIM

   -- 

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   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/Support/Mailing_Lists/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/Support/Mailing_Lists

-- 
Ahmet YILDIRIM

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-908

Re: [gmx-users] Box size and potential energy calculation

2011-01-21 Thread Mark Abraham


On 21/01/2011 6:47 AM, Christian Mötzing wrote:

Hi,

I currently read through the GMX manual 4.5.3. I have two questions:

1) Density is calculated by the density of the material and the box
volume. But I can't find a reference on how the box size is calculated.
Can you point me to some literature?


The volume of the box is the determinant of the matrix formed by the box 
vectors. If that matrix is upper- or lower-triangular, then the volume 
is the product of the entries in the leading diagonal.



2) I wanted to look up the calculation of the potential energy. Do I
understand the calculation correctly:
- pairwise sum over all molecules
- for each pair Coulomb, Lennard-Jones and bonded terms are summed
aswell
- the calculation involves the position of the molecules (for example
Lennard-Jones)


Well that's vaguely accurate. Bonded terms can involve more than pairs 
of atoms.


Mark
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Re: [gmx-users] Fwd: RMSD calculation of a specific region

2011-01-21 Thread bharat gupta

On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>>
>>
>> I want to calculate the rmsd of amino acid 65 to 67 of two simulated
>> proteins with  loop replacement in another one to find out how the position
>> of these 3  amino acids change due to the replacement of a loop region in
>> same protein ... How can I achieve it with gromacs...
>>
>>
> Use g_rms with a suitable index group.
>
> -Justin
>
>  --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.com 
>>
>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.com 
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>


I am not able to search some relevant document about creating index group
fro g_rms ... I found one i gromacs website
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
but
this link doesnot explain much about it ... can u pls guide me to some
relevant link ??


I am stating my question here again :  I want to calculate the rmsd of amino
acid 65 to 67 of two simulated proteins with  loop replacement in another
one to find out how the position of these 3  amino acids change due to the
replacement of a loop region in same protein ... How can I achieve it with
gromacs...


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] Fwd: RMSD calculation of a specific region

2011-01-21 Thread Justin A. Lemkul

bharat gupta wrote:

On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul > wrote:

bharat gupta wrote:

I want to calculate the rmsd of amino acid 65 to 67 of two
simulated proteins with  loop replacement in another one to find
out how the position of these 3  amino acids change due to the
replacement of a loop region in same protein ... How can I
achieve it with gromacs...

Use g_rms with a suitable index group.

-Justin

-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 
>

-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 
>

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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I am not able to search some relevant document about creating index 
group fro g_rms ... I found one i gromacs website 
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive but 
this link doesnot explain much about it ... can u pls guide me to some 
relevant link ??

See the manual, section 8.1 and appendix D.83.  If you search the Gromacs site 
for "index group" you will find (among others):

http://www.gromacs.org/Documentation/File_Formats/Index_File

-Justin

I am stating my question here again :  I want to calculate the rmsd of 
amino acid 65 to 67 of two simulated proteins with  loop replacement in 
another one to find out how the position of these 3  amino acids change 
due to the replacement of a loop region in same protein ... How can I 
achieve it with gromacs...

--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] charge group radii larger that rlist-rvdw

2011-01-21 Thread Kavyashree M

Sir,

 System is a protein with 123 aa. No modifications were made on the pdb
file,
and it was submitted to pdb2gmx by removing all HETATMs, retaining only
protein
atoms. topology was created entirely by pdb2gmx and no other molecule was
introduced.

 I will go through the OPLSAA paper, but if I increase rlist to 1.4nm
without reducing
rvdw according to "The Origin of Layer Structure Artifacts in Simulations of
Liquid Water"
- JCTC, 2006, 2, 1-11, will it not cause orderedwater shell during
simultion?


Thanking you
M. Kavyashree

On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Sir,
>>
>>   What exactly can be wrong with the topology? As I tried with
>>
>
> I don't know, what's in your system?  Was the topology created entirely by
> pdb2gmx, or have you introduced some other molecules that you've
> parameterized?
>
>
>  different PDBs of same structure at higher resolutions too, I am getting
>> almost similar charge group radii, so can you kindly elaborate about
>> what can go wrong in the topology to get such values?
>>
>>
> Large charge groups indicate that a fair number of atoms have been included
> in the same charge group.  Usually only two or three atoms are in a charge
> group, rendering them fairly small.  With PME, the effects may not be that
> large, i.e.
> http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html,
> but it's still worth investigating what your largest charge group is that's
> causing this problem.  If the topology is sound and is based entirely upon
> standard force field files, it may suffice to simply increase rlist to 1.4
> nm, leaving all the other cutoffs at 1.0, which I believe is standard for
> OPLS (but don't just take my word for it).
>
> -Justin
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 mailing listgmx-users@gromacs.org
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[gmx-users] DSPC all atom .itp file

2011-01-21 Thread Anirban Ghosh

Hi ALL,

Can anyone please send me an all-atom DSPC .itp file at *
reach.anirban.gh...@gmail.com *or* anirba...@gmail.com*
*
*
Thanks a lot.


-Anirban
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[gmx-users] Re: Problem with using topolbuild1_3.tgz

2011-01-21 Thread Sweta Iyer

> Send gmx-users mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. OPLS implicit solvent problems (francesca.stanzi...@unina.it)
>2. Re: OPLS implicit solvent problems (Per Larsson)
>3. (no subject) (francesca.stanzi...@unina.it)
>4. CG to FG transformation error (Anirban Ghosh)
>5. Re: Problem with using topolbuild1_3.tgz (Bruce D. Ray)
>
>
> --
>
> Message: 1
> Date: Fri, 21 Jan 2011 13:51:08 +0100
> From: francesca.stanzi...@unina.it
> Subject: [gmx-users] OPLS implicit solvent problems
> To: gmx-users@gromacs.org
> Message-ID: <20110121135108.kg4c6rbjr44kg...@webmail.unina.it>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>Hello,
>
>I try to perform an implicit solvent simulation with Gromacs 4.5.3.
> version. I have a system corresponding to 6 peptides generated by
> Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA
> and i put the N-and C- termini as NH2 and COOH. My topology file is
> correct, and is all systems are included.
>
>; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp" ---> in this .itp file is
> included gbsa.itp
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
>
> ; Include water topology
> #include "./oplsaa.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcx    fcy    fcz
>    1    1   1000   1000   1000
> #endif
>  
> ; Include topology for ions
> #include "./oplsaa.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound    #mols
> Protein_chain_A 1
> Protein_chain_B 1
> Protein_chain_C 1
> Protein_chain_D 1
> Protein_chain_E 1
> Protein_chain_F 1
> -
>
>When I start my simulations (md_start.mdp) in implicit solvent, i
> have this fatal error:
>
>GB parameter(s) missing or negative for atom type 'opls_912B'
>
> GB parameter(s) missing or negative for atom type 'opls_267'
>
> GB parameter(s) missing or negative for atom type 'opls_269'
>
> GB parameter(s) missing or negative for atom type 'opls_268'
>
> GB parameter(s) missing or negative for atom type 'opls_270'
>
>Program grompp, VERSION 4.5.3
> Source code file: grompp.c, line: 1123
>
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 5 atomtypes or they might be
> negative.
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors.
>
>
> 
>
>Controlling these atoms they corresponding to:
>
>opls_912B= the  CA of N-terminal residue
>
>opls_267= Co in COOH
>
>opls_268= Oh in COOH
>
>opls_269= Oc in COOH neutral
>
>opls_270= H in COOH
>
>
>
>in the file gbsa.itp in opls.ff directory these atoms missing. Now,
> have I done something wrong? If is all ok, is it possible to create
> these missing atoms in the gbsa.itp file?
>
>thanx,
>
>francesca stanzione
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/10a6228e/attachment-0001.html
>
> --
>
> Message: 2
> Date: Fri, 21 Jan 2011 14:11:40 +0100
> From: Per Larsson 
> Subject: Re: [gmx-users] OPLS implicit solvent problems
> To: Discussion list for GROMACS users 
> Message-ID: <6ec741e6

[gmx-users] doubts on g_confrms output

2011-01-21 Thread Kwee Hong

Hi,


I was trying to do some analysis following John's "GROMACS tutorial for 
solvation study of spider toxin peptide".
I'm using GROMACS-4.5.3 and my command line for g_confrms is 

g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb

The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, 
when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in 
a 
mess. And when I tried it out with pymol, I can only visualised one model. 
Model 
2 did not appear. I wonder would it be the pdb format generated by g_confrms is 
not the standard pdb format and had caused VMD and final failed to read  them?

Herein, I attached part of the pdb file generated by  fit_wet.pdb. Any insight 
is welcomed.

Thanks,
Joyce




fit_wet.pdb
Description: Binary data
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Re: [gmx-users] doubts on g_confrms output

2011-01-21 Thread Tsjerk Wassenaar

Hi Joyce,

In pymol use 'set all_states'

Cheers,

Tsjerk

On Jan 22, 2011 8:30 AM, "Kwee Hong"  wrote:

Hi,

I was trying to do some analysis following John's "GROMACS tutorial for
solvation study of spider toxin peptide".
I'm using GROMACS-4.5.3 and my command line for g_confrms is

g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb

The program calculated the RMSD sucessfully and fit_wet.pdb was generated.
Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is
obviously in a mess. And when I tried it out with pymol, I can only
visualised one model. Model 2 did not appear. I wonder would it be the pdb
format generated by g_confrms is not the standard pdb format and had caused
VMD and final failed to read them?

Herein, I attached part of the pdb file generated by fit_wet.pdb. Any
insight is welcomed.

Thanks,
Joyce



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[gmx-users] Fwd: RMSD calculation of a specific region

[gmx-users] fatal error

[gmx-users] charge group radii larger that rlist-rvdw

[gmx-users] Error in generating DPPC using grompp

Re: [gmx-users] Fwd: RMSD calculation of a specific region

Re: [gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did

[gmx-users] Pull code

Re: [gmx-users] charge group radii larger that rlist-rvdw

Re: [gmx-users] fatal error

Re: [gmx-users] Error in generating DPPC using grompp

Re: [gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did

[gmx-users] DSPC all atom .itp file

[gmx-users] OPLS implicit solvent problems

Re: [gmx-users] OPLS implicit solvent problems

[gmx-users] (no subject)

[gmx-users] CG to FG transformation error

Re: [gmx-users] Problem with using topolbuild1_3.tgz

Re: [gmx-users] CG to FG transformation error

Re: [gmx-users] charge group radii larger that rlist-rvdw

Re: [gmx-users] charge group radii larger that rlist-rvdw

[gmx-users] RNA with small molecule

Re: [gmx-users] RNA with small molecule

Re: [gmx-users] RNA with small molecule

Re: [gmx-users] RNA with small molecule

Re: [gmx-users] fatal error

Re: [gmx-users] fatal error

Re: [gmx-users] fatal error

Re: [gmx-users] fatal error

Re: [gmx-users] Box size and potential energy calculation

Re: [gmx-users] Fwd: RMSD calculation of a specific region

Re: [gmx-users] Fwd: RMSD calculation of a specific region

Re: [gmx-users] charge group radii larger that rlist-rvdw

[gmx-users] DSPC all atom .itp file

[gmx-users] Re: Problem with using topolbuild1_3.tgz

[gmx-users] doubts on g_confrms output

Re: [gmx-users] doubts on g_confrms output

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