Re: [gmx-users] difference in potenital energy on desktop and server run

[gupta.rakesh082]

EM RUN

Steepest Descents converged to machine precision in 2820 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.9268122e+05
Maximum force =  1.9479546e+02 on atom 123
Norm of force =  6.3931437e+00

grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -v -deffnm min
 
g_energy -f min.edr -o npt_potenital.xvg
10 0

Statistics over 2818 steps [ 0. through 2817. ps ], 1 data sets
All statistics are over 2225 points (frames)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -287434   28006986.15   -18110.5 
(kJ/mol)



NPT RUN

grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr
mdrun -nt 8 -c -v -deffnm NPT 

g_energy -f NPT.edr -o npt_potenital.xvg
10 0

Statistics over 1001 steps [ 0. through 2. ps ], 1 data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential168770   130031030.1   -6644.57 
(kJ/mol)

I am surprised to see that at such huge potential energy my simulation box
is still stable. 

Desktop Run

I took generated NPT.gro file in previous run and performed a small 200 ps
npt simulation on my desktop machine using following commmand.

grompp -f NPT.mdp -c NPT.gro -p cer.itp -o NPTdesktop.tpr
mdrun --c -v -deffnm NPTdesktop

g_energy -f NPTdesktop.edr -o NPTdesktop_potential.xvg

Statistics over 11 steps [ 0. through 200. ps ], 1 data sets
All statistics are over 1001 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -234831 47582.555117.566 
(kJ/mol)

This time potential energy became negative after few ps and converse to
value around order of ~ -2x 10^5.



  


 







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Re: [gmx-users] difference in potenital energy on desktop and server run

[gupta.rakesh082]

EM RUNSteepest Descents converged to machine precision in 2820 steps,but did
not reach the requested Fmax < 10.Potential Energy  = -2.9268122e+05Maximum
force =  1.9479546e+02 on atom 123Norm of force = 
6.3931437e+00grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tprmdrun -c
-v -deffnm min g_energy -f min.edr -o npt_potenital.xvg10 0Statistics over
2818 steps [ 0. through 2817. ps ], 1 data setsAll statistics are
over 2225 points (frames)Energy  Average   Err.Est.  
RMSD 
Tot-Drift---Potential
  
-287434   28006986.15   -18110.5  (kJ/mol)NPT RUNgrompp -f NPT.mdp
-c min.gro -p cer.itp -o NPT.tprmdrun -nt 8 -c -v -deffnm NPT g_energy -f
NPT.edr -o npt_potenital.xvg10 0Statistics over 1001 steps [ 0.
through 2. ps ], 1 data setsAll statistics are over 11
pointsEnergy  Average   Err.Est.   RMSD 
Tot-Drift---Potential
   
168770   130031030.1   -6644.57  (kJ/mol)I am surprised to see that
at such huge potential energy my simulation box is still stable. Desktop
RunI took generated NPT.gro file in previous run and performed a small 200
ps npt simulation on my desktop machine using following commmand.grompp -f
NPT.mdp -c NPT.gro -p cer.itp -o NPTdesktop.tprmdrun --c -v -deffnm
NPTdesktopg_energy -f NPTdesktop.edr -o NPTdesktop_potential.xvgStatistics
over 11 steps [ 0. through 200. ps ], 1 data setsAll statistics
are over 1001 pointsEnergy  Average   Err.Est.  
RMSD 
Tot-Drift---Potential
  
-234831 47582.555117.566  (kJ/mol)This time potential energy
became negative after few ps and converse to value around order of ~ -2x
10^5.   

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Re: [gmx-users] C-terminus residue name in Gromos43a1

[Francesca Vitalini]

Residue 2 is just alanine,the most standard amino acid ever.

Any help?

Francesca.
 Il 26/feb/2014 11:58 "Justin Lemkul"  ha scritto:

>
>
> On 2/26/14, 4:08 AM, Francesca Vitalini wrote:
>
>> Dear Justin
>>
>>
>> 2014-02-25 19:07 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
>>>
>>>  Dear Justin,

 Thanks for your answer.
 However I noticed that I had made a mistake and there is no definition
 of
 NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at.

 So defining a new residue-type in the rtp file is not as trivial as I
 had
 hoped.
 I followed the instructions given on the GROMACS wab page
 http://www.gromacs.org/Documentation/How-tos/Adding_
 a_Residue_to_a_Force_Field

 and copied the gromos43a1.ff folder and the residuetypes.dat file in my
 local directory.
 I have added the following definition of NAC to the
 gromos43a1.ff/aminoacids.rtp file

 [ NAC ]
[ atoms ]
   N N-0.28000 0
   H H 0.28000 0
  CA   CH3 0.0 0
[ bonds ]
   NCAgb_20
   N Hgb_2


>>> You're missing a bond here, from N to -C.
>>>
>>
>>
>> I hadn't add that as all the other residue types also don't have it
>> defined. It seems to me that the bond is defined as C to N+ not the other
>> way round. In this case however I have no N+ and the hydrogens are not
>> defined, so how can I properly define that bond?
>>
>> I also tried to define the bond N to -C as gb_9 (ie the bond type of C to
>> N+) but it leads to the exact same error message.
>>
>>
> Ah, true, this isn't necessary.
>
>
>>
>>> [ angles ]
>>>
 ;  aiajak   gromos type
  -C N H ga_31
   H NCA ga_17
  -C NCA ga_30
[ impropers ]
 ;  aiajakal   gromos type
   N-CCA H gi_1
[ dihedrals ]
 ;  aiajakal   gromos type
 -CA-C NCA gd_4

 and then tried again the pdb2gmx command as following and obtained this
 error
 Fatal error:
 There is a dangling bond at at least one of the terminal ends. Select a
 proper terminal entry.
 For more information and tips for troubleshooting, please check the
 GROMACS
 website at http://www.gromacs.org/Documentation/Errors


 Evidently I have not defined correctly my NAC residue. However, I am not
 sure of how to correctly define the bonds in this specific case. Could
 you
 possibly identify the error and/or point me where to find detailed
 information? I have already looked at the manual but haven't been able
 to
 come up with successful definition.


  You need to use pdb2gmx -ter and select "None" for the C-terminus,
>>> otherwise pdb2gmx tries to build a carboxylate.  When it can't find the
>>> atoms it needs to do this, it fails.
>>>
>>>
>> I do use the -ter "None" option for both termini and the error is still
>> present. What I find interesting is this part of the pdb2gmx output
>>
>> Select start terminus type for ACE-1
>>   0: NH3+
>>   1: NH2
>>   2: None
>> 2
>> Start terminus ACE-1: None
>> Select end terminus type for ACE-1
>>   0: COO-
>>   1: COOH
>>   2: None
>> 2
>> End terminus ACE-1: None
>>
>>
>> where it looks like that ACE is the end terminus, not NAC, despite my pdb
>> looks like the following. Any suggestions?
>>
>>
> What is residue 2?  Is it anything non-standard?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] Martini Lo-phase has gel-like properties

[David Ackerman]

Hello Everyone,

I have been using the Martini CG forcefield to simulate phase separation in
a bilayer containing DPPC/DUPC/Chol at a ratio of 1:1:.5. Though this does
phase separate at 295 K, when I use mdp files based on
http://md.chem.rug.nl/cgmartini/images/parameters/exampleMDP/martini_v2.x_example.mdp,
the Lo phase has gel-like properties. Correlation functions between
cholesterols in the Lo phase persist for upwards of 10 nm, diffusion of Lo
lipids deep within the Lo phase (when corrected by subtracting the center
of mass motion of the bulk Lo phase) is on the order of 5E-10 cm^2/s.
Additionally, area per lipid are smaller and orders higher for Lo lipids
than would be expected.

Based on Waheed et al., Biophys. J, 103 (2012), it seems that the Lo-gel
transition temperature for a DPPC/Chol bilayer is ~ 300 K or more (when
cholesterol concentration is > 20%). However many Martini papers simulating
coexisting Lo/Ld patches with similar cholesterol concentrations do so at
295 K, as I have also tried. What I am finding however is that the Lo
phases I get at these temperatures is very gel-like. I have also seen the
aforementioned persistent correlations using the raft parameter files
provided at
http://md.chem.rug.nl/cgmartini/index.php/example-applications2/lipid-membranes
.

I am curious as to whether or not others have experienced these or similar
issues, or could provide any insights. I have copied an example mdp file
below.

Thank you,
David
__

title= Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable
; with dt=40 fs, some (especially rings and polarizable water) require
20-30 fs.
; Note that time steps of 40 fs and larger may create local heating or
; cooling in your system. Although the use of a heat bath will globally
; remove this effect, it is advised to check consistency of
; your results for somewhat smaller time steps in the range 20-30 fs.
; Time steps exceeding 40 fs should not be used; time steps smaller
; than 20 fs are also not required unless specifically stated in the itp
file.

integrator   = md
dt   = 0.02
nsteps   = 125000
nstcomm  = 10
comm-grps=

nstxout  = 25
nstvout  = 25
nstfout  = 0
nstlog   = 25
nstenergy= 25
nstxtcout= 0
xtc_precision= 0
xtc-grps =
energygrps   = DPPC DUPC CHOL W

; NEIGHBOURLIST and MARTINI
; Due to the use of shifted potentials, the noise generated
; from particles leaving/entering the neighbour list is not so large,
; even when large time steps are being used. In practice, once every
; ten steps works fine with a neighborlist cutoff that is equal to the
; non-bonded cutoff (1.2 nm). However, to improve energy conservation
; or to avoid local heating/cooling, you may increase the update frequency
; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
; is computationally less expensive and leads to improved energy
conservation

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2

; MARTINI and NONBONDED
; Standard cut-off schemes are used for the non-bonded interactions
; in the Martini model: LJ interactions are shifted to zero in the
; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
; The treatment of the non-bonded cut-offs is considered to be part of
; the force field parameterization, so we recommend not to touch these
; values as they will alter the overall balance of the force field.
; In principle you can include long range electrostatics through the use
; of PME, which could be more realistic in certain applications
; Please realize that electrostatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit
screening
; in aqueous environment. In this case, the use of PME is more realistic.
;
; For use in combination with the Verlet-pairlist algorithm implemented
; in Gromacs 4.6 a straight cutoff in combination with the potential
; modifiers can be used. Although this will change the potential shape,
; preliminary results indicate that forcefield properties do not change a
lot
; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
; your particular system. The advantage is a gain of speed of 50-100%.

coulombtype  = Shift

[gmx-users] Martini Lo-phase seems gel-like

[David Ackerman]

Hello Everyone,

I have been using the Martini CG forcefield to simulate phase separation in
a bilayer containing DPPC/DUPC/Chol at a ratio of 1:1:.5. Though this does
phase separate at 295 K, when I use mdp files based on
http://md.chem.rug.nl/cgmartini/images/parameters/exampleMDP/martini_v2.x_example.mdp,
the Lo phase has gel-like properties. Correlation functions between
cholesterols in the Lo phase persist for upwards of 10 nm, diffusion of Lo
lipids deep within the Lo phase (when corrected by subtracting the center
of mass motion of the bulk Lo phase) is on the order of 5E-10 cm^2/s.
Additionally, area per lipid are smaller and orders higher for Lo lipids
than would be expected.

Based on Waheed et al., Biophys. J, 103 (2012), it seems that the Lo-gel
transition temperature for a DPPC/Chol bilayer is ~ 300 K or more (when
cholesterol concentration is > 20%). However many Martini papers simulating
coexisting Lo/Ld patches with similar cholesterol concentrations do so at
295 K, as I have also tried. What I am finding however is that the Lo
phases I get at these temperatures is very gel-like. I have also seen the
aforementioned persistent correlations using the raft parameter files
provided at
http://md.chem.rug.nl/cgmartini/index.php/example-applications2/lipid-membranes
.

I am curious as to whether or not others have experienced these or similar
issues, or could provide any insights. I have copied an example mdp file
below.

Thank you,
David
__

title= Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable
; with dt=40 fs, some (especially rings and polarizable water) require
20-30 fs.
; Note that time steps of 40 fs and larger may create local heating or
; cooling in your system. Although the use of a heat bath will globally
; remove this effect, it is advised to check consistency of
; your results for somewhat smaller time steps in the range 20-30 fs.
; Time steps exceeding 40 fs should not be used; time steps smaller
; than 20 fs are also not required unless specifically stated in the itp
file.

integrator   = md
dt   = 0.02
nsteps   = 125000
nstcomm  = 10
comm-grps=

nstxout  = 25
nstvout  = 25
nstfout  = 0
nstlog   = 25
nstenergy= 25
nstxtcout= 0
xtc_precision= 0
xtc-grps =
energygrps   = DPPC DUPC CHOL W

; NEIGHBOURLIST and MARTINI
; Due to the use of shifted potentials, the noise generated
; from particles leaving/entering the neighbour list is not so large,
; even when large time steps are being used. In practice, once every
; ten steps works fine with a neighborlist cutoff that is equal to the
; non-bonded cutoff (1.2 nm). However, to improve energy conservation
; or to avoid local heating/cooling, you may increase the update frequency
; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
; is computationally less expensive and leads to improved energy
conservation

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2

; MARTINI and NONBONDED
; Standard cut-off schemes are used for the non-bonded interactions
; in the Martini model: LJ interactions are shifted to zero in the
; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm.
; The treatment of the non-bonded cut-offs is considered to be part of
; the force field parameterization, so we recommend not to touch these
; values as they will alter the overall balance of the force field.
; In principle you can include long range electrostatics through the use
; of PME, which could be more realistic in certain applications
; Please realize that electrostatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit
screening
; in aqueous environment. In this case, the use of PME is more realistic.
;
; For use in combination with the Verlet-pairlist algorithm implemented
; in Gromacs 4.6 a straight cutoff in combination with the potential
; modifiers can be used. Although this will change the potential shape,
; preliminary results indicate that forcefield properties do not change a
lot
; when the LJ cutoff is reduced to 1.1 nm. Be sure to test the effects for
; your particular system. The advantage is a gain of speed of 50-100%.

coulombtype  = Shift

Re: [gmx-users] how to increase vacuum thickness in a periodic system

[Dr. Vitaly Chaban]

editconf -box X Y Z


Dr. Vitaly V. Chaban


On Wed, Feb 26, 2014 at 7:58 PM, decaiyu  wrote:
> Dear All,
>
> I ran a NVT simulation with a layer of oil+vaccuum.
> Because of periodic boundary condition, there are some molecules on the top
> of vaccuum layer.
> Now I want to increase the vaccum thickness so that I can add some water in
> it.
> Is there a simple way to do that?
> The molecules on the top of the layer causes some trouble.
>
> Regards,
> Decai
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/how-to-increase-vacuum-thickness-in-a-periodic-system-tp5014828.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] how to increase vacuum thickness in a periodic system

[decaiyu]

Dear All,

I ran a NVT simulation with a layer of oil+vaccuum.
Because of periodic boundary condition, there are some molecules on the top
of vaccuum layer.
Now I want to increase the vaccum thickness so that I can add some water in
it.
Is there a simple way to do that?
The molecules on the top of the layer causes some trouble.

Regards,
Decai

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Re: [gmx-users] difference in potenital energy on desktop and server run

[Justin Lemkul]

On 2/26/14, 10:50 AM, gupta.rakesh082 wrote:

I am using gromacs 4.6.5. Surprisingly system is stable at such high
potential energy. I created bilayer system using packmol then solvated it
with water using genbox.

I did energy minimization using following command

grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -v -deffnm min

The resulted potential energy of system was negative (~ 2x 10^-5 ).

Then I performed NPT run using following command

grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr
mdrun -c -v -deffnm NPT

The resulted structure and system was stable but the potential energy of
the system was highly positvie (~ 10^5).



Do you see a massive expansion of box vectors during NPT?  Such a net repulsive 
potential should cause the system to expand quite dramatically.



Just for curiosity I took resulted NPT.gro structure and ran NPT simulation
on my desktop which has same version of GROMACS (same precision).
Surprisingly the total energy was negative after few ps run and converse to
around order of ~ -10^5.

I have attached my input .mdp files for energy minimization and NPT MD run.



The list doesn't accept attachments.  You can just copy and paste their 
contents.  The .mdp files are less critical than actual screen output from:


1. Energy minimization (Epot, Fmax, etc)
2. The output of g_energy on npt.edr (Potential energy with RMSD, box vectors, 
and anything else you are examining)


You've got some inconsistencies in notation above that I am assuming are typos, 
but to be 100% we are on the same page, I need to see the exact 
(copied-and-pasted-from-terminal) output that you are getting.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] difference in potenital energy on desktop and server run

[gupta.rakesh082]

I am using gromacs 4.6.5. Surprisingly system is stable at such high
potential energy. I created bilayer system using packmol then solvated it
with water using genbox.

I did energy minimization using following command

grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -v -deffnm min

The resulted potential energy of system was negative (~ 2x 10^-5 ).

Then I performed NPT run using following command

grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr
mdrun -c -v -deffnm NPT

The resulted structure and system was stable but the potential energy of
the system was highly positvie (~ 10^5).

Just for curiosity I took resulted NPT.gro structure and ran NPT simulation
on my desktop which has same version of GROMACS (same precision).
Surprisingly the total energy was negative after few ps run and converse to
around order of ~ -10^5.

I have attached my input .mdp files for energy minimization and NPT MD run.



On Wed, Feb 26, 2014 at 4:41 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5014819...@n6.nabble.com> wrote:

>
>
> On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:
> > Dear allI performed MD simulation of lipid bilayer on my desktop it is
> giving
> > correct results and negative potential energy (~ -10^5) but when I ran
> the
> > same simulation on a server using multi thread (-nt 8), It is giving
> > positive potential energy (~ 10^5). Initially I thought it might be
> problem
> > with mpi to check this I ran simulation on cluster with single thread
> but
> > still potential energy is positive.Any help would be appreciated
> >
>
> If the potential energy was that high, I would suspect the system crashed
> - did
> it?  What were you running, EM or MD?  If the latter, did you provide the
> correct, energy-minimized structure to grompp when creating the .tpr file
> for
> the run?  Detailed commands and actual output would be useful here,
> otherwise
> it's all guesswork.
>
> Also, what version of Gromacs are you using?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [hidden email]  |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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--
Regards
RAKESH GUPTA
==
ME- Chemical Engineering
Indian Institute of Science
Bangalore-560012
===
(M) +91-9611187322


npt.mdp (3K) 
em.mdp (1K) 


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Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield

[Justin Lemkul]

On 2/26/14, 7:05 AM, lalithkumar wrote:

Dear Dr. Justin,

Thank you for pointing out the details of error. I have missed out the
version of GROMACS I have been using and so I would like to let you know
that my version is 4.5.7. In this version ffnonbonded.itp file of the
gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I


I doubt that's correct; every Gromacs version I've ever had contained 
[pairtypes] in this file.  Check again.  I don't have 4.5.7 installed anywhere, 
but in 4.6.x (several versions), it is clearly present.



should agree that I dont know how they can be generated and to specify
manually. So, in a crude way I can say that I have copied all the LJ 14
types from the ffG43a1p forcefield at the gromacs contributors link:
http://www.gromacs.org/Downloads/User_contributions/Force_fields

This includes the following addition lines:

; begin insert from pamac_hsnnb.itp
; [ pairtypes ]
; for LJ 14 - use same for OP as for OA
   OPO  1  0.0022619536  9.687375e-07
   OP   OM  1  0.0022619536  9.687375e-07
   OP   OP  1  0.0022619536  1.265625e-06
   OW   OP  1  0.0024331696   1.737e-06
N   OP  1  0.0023475616  1.463625e-06
   NT   OP  1  0.0023475616  1.463625e-06
   NL   OP  1  0.0023475616  1.463625e-06
   NR   OP  1  0.0023475616  1.463625e-06
   NZ   OP  1  0.0023475616  1.463625e-06
   NE   OP  1  0.0023475616  1.463625e-06
C   OP  1  0.0023009528  2.066625e-06
  CH1   OP  1  0.0025663376  2.174625e-06
  CH2   OP  1  0.0032687988  3.000375e-06
  CH3   OP  1  0.0039370168  3.907125e-06
  CH4   OP  1  0.005459888  6.59475e-06
  CR1   OP  1  0.003536086  3.24675e-06
   HC   OP  1  0.000437552  1.38375e-07
H   OP  1   0   0
  DUM   OP  1   0   0
S   OP  1  0.0047521952   4.068e-06
 CU1+   OP  1  0.000972602  8.053875e-08
 CU2+   OP  1  0.000972602  8.053875e-08
   FE   OP  1   0   0
 ZN2+   OP  1  0.000972602  1.09305e-07
 MG2+   OP  1  0.0003842848  6.56775e-08
 CA2+   OP  1  0.001507652  7.939125e-07
P   OP  1  0.005773784  5.299875e-06
   AR   OP  1  0.003764374  3.53025e-06
F   OP  1  0.0016322592  9.81225e-07
   CL   OP  1  0.0044525672  4.399875e-06
   BR   OP  1  0.0016332104  9.1035e-06
 CMET   OP  1  0.0044806276  5.1373125e-06
 OMET   OP  1  0.0022619536  1.265625e-06
  NA+   OP  1  0.00040373684  1.63125e-07
  CL-   OP  1   0.0055883  1.16325e-05
 CCHL   OP  1  0.0024394475   2.268e-06
CLCHL   OP  1  0.004334666  4.1738625e-06
 HCHL   OP  1  0.0002920184  7.377075e-08
SDMSO   OP  1  0.0048877412  5.216175e-06
CDMSO   OP  1  0.0045248108  5.2475625e-06
ODMSO   OP  1  0.0022663291  9.752175e-07
 CCL4   OP  1  0.0024394475  3.1014e-06
CLCL4   OP  1  0.0041472796  4.01985e-06
   SI   OP  1   0   0
; end insert from pamac_hsnnb.itp

And I had copied them as is to my ffnonbonded.itp file in modified
gromos53a6.ff folder. Also, I have also modified atomtypes as per latest
versions (for example CMET to CMet).

Finally, I could pass the grompp set now and can run mdrun too successfully.
Now I need your valuable review to know whether I had done is correct or can
I do better than this way. If so please suggest some helping material
regarding process of setting user defined LJ 14 pair types interactions to
gromos53a6ff or any forcefield. And also, briefly comment on how difference
with my results by doing in the method mentioned by me and with any other
suggested method from your side.

Please let me know if any further information to be provided from my side



What you've done is not correct.  You've made a mixed force field that is not 
necessarily viable.  You need proper parameters within a single force field, not 
borrowed from some other parameter set, unless you can demonstrate through 
rigorous testing and validation that what you've done is correct.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield

[lalithkumar]

Dear Dr. Justin,

Thank you for pointing out the details of error. I have missed out the
version of GROMACS I have been using and so I would like to let you know
that my version is 4.5.7. In this version ffnonbonded.itp file of the
gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I
should agree that I dont know how they can be generated and to specify
manually. So, in a crude way I can say that I have copied all the LJ 14
types from the ffG43a1p forcefield at the gromacs contributors link:
http://www.gromacs.org/Downloads/User_contributions/Force_fields

This includes the following addition lines:

; begin insert from pamac_hsnnb.itp
; [ pairtypes ]
; for LJ 14 - use same for OP as for OA 
  OPO  1  0.0022619536  9.687375e-07
  OP   OM  1  0.0022619536  9.687375e-07
  OP   OP  1  0.0022619536  1.265625e-06
  OW   OP  1  0.0024331696   1.737e-06
   N   OP  1  0.0023475616  1.463625e-06
  NT   OP  1  0.0023475616  1.463625e-06
  NL   OP  1  0.0023475616  1.463625e-06
  NR   OP  1  0.0023475616  1.463625e-06
  NZ   OP  1  0.0023475616  1.463625e-06
  NE   OP  1  0.0023475616  1.463625e-06
   C   OP  1  0.0023009528  2.066625e-06
 CH1   OP  1  0.0025663376  2.174625e-06
 CH2   OP  1  0.0032687988  3.000375e-06
 CH3   OP  1  0.0039370168  3.907125e-06
 CH4   OP  1  0.005459888  6.59475e-06
 CR1   OP  1  0.003536086  3.24675e-06
  HC   OP  1  0.000437552  1.38375e-07
   H   OP  1   0   0
 DUM   OP  1   0   0
   S   OP  1  0.0047521952   4.068e-06
CU1+   OP  1  0.000972602  8.053875e-08
CU2+   OP  1  0.000972602  8.053875e-08
  FE   OP  1   0   0
ZN2+   OP  1  0.000972602  1.09305e-07
MG2+   OP  1  0.0003842848  6.56775e-08
CA2+   OP  1  0.001507652  7.939125e-07
   P   OP  1  0.005773784  5.299875e-06
  AR   OP  1  0.003764374  3.53025e-06
   F   OP  1  0.0016322592  9.81225e-07
  CL   OP  1  0.0044525672  4.399875e-06
  BR   OP  1  0.0016332104  9.1035e-06
CMET   OP  1  0.0044806276  5.1373125e-06
OMET   OP  1  0.0022619536  1.265625e-06
 NA+   OP  1  0.00040373684  1.63125e-07
 CL-   OP  1   0.0055883  1.16325e-05
CCHL   OP  1  0.0024394475   2.268e-06
   CLCHL   OP  1  0.004334666  4.1738625e-06
HCHL   OP  1  0.0002920184  7.377075e-08
   SDMSO   OP  1  0.0048877412  5.216175e-06
   CDMSO   OP  1  0.0045248108  5.2475625e-06
   ODMSO   OP  1  0.0022663291  9.752175e-07
CCL4   OP  1  0.0024394475  3.1014e-06
   CLCL4   OP  1  0.0041472796  4.01985e-06
  SI   OP  1   0   0
; end insert from pamac_hsnnb.itp

And I had copied them as is to my ffnonbonded.itp file in modified
gromos53a6.ff folder. Also, I have also modified atomtypes as per latest
versions (for example CMET to CMet).

Finally, I could pass the grompp set now and can run mdrun too successfully.
Now I need your valuable review to know whether I had done is correct or can
I do better than this way. If so please suggest some helping material
regarding process of setting user defined LJ 14 pair types interactions to
gromos53a6ff or any forcefield. And also, briefly comment on how difference
with my results by doing in the method mentioned by me and with any other
suggested method from your side.

Please let me know if any further information to be provided from my side

Thank you 

With kind regards,
Lalith

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Re: [gmx-users] please guide me through the confusing gromacs results!!!

[Dr. Vitaly Chaban]

if the system sends a termination request to MDRUN, it stops the main
cycle and writes down the summary of the run.


Dr. Vitaly V. Chaban


On Wed, Feb 26, 2014 at 10:31 AM, delara aghaie  wrote:
> Dear Gromacs users,
> we want to simulateHSA protein using8 processors. Usually with our available 
> system 10ns simulation on 8 processors lasts 2-3 days.
> This time we submitted 10 ns simulation, after almost 6 days it has finished 
> but when we look at md.log file, only 179411 steps has been completed and all 
> the averages are over this time, although we have submitted the run 500 
> steps=10ns
> 1) First I want to know how the log file shows the end of simulation, 
> although only 0.35 ns of simulation is done and if we draw RDF the time again 
> shows completing of 0.35 ns.
> you can see the ending part of log file below:
> 2) the second point is that the average load imbalance is shown as 110.3% 
> while for previous runs we had this as 3-4 %.
> what can be the reason for this high load imbalance?
> and is this responsible for the lower simulation efficiency and higher time?
> and the most important that why the log file is written in the way that the 
> simulation has been completed while only 0.3 ns has passes?
> Thanks for your time
> **
>  D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
>
>  av. #atoms communicated per step for force:  2 x 97992.1
>  av. #atoms communicated per step for LINCS:  2 x 2373.8
>
>  Average load imbalance: 110.3 %
>  Part of the total run time spent waiting due to load imbalance: 1.4 %
>
>
>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes Number G-CyclesSeconds %
> ---
>  Domain decomp. 8  35882   556174.638   209101.4 5.1
>  DD comm. load  8359  235.791   88.6 0.0
>  Comm. coord.   8 179411   407595.614   153241.1 3.7
>  Neighbor search8  3588339333.69814788.0 0.4
>  Force  8 179411   205203.39377149.0 1.9
>  Wait + Comm. F 8 179411   471040.171   177093.9 4.3
>  PME mesh   8 179411  8699277.459  3270611.079.1
>  Write traj.875215563.463 5851.3 0.1
>  Update 8 17941112991.140 4884.2 0.1
>  Constraints8 179411   438837.169   164986.8 4.0
>  Comm. energies 8  35884   149298.11156130.6 1.4
>  Rest   86090.776 2289.9 0.1
> ---
>  Total  811001641.424  4136215.9   100.0
> ---
> ---
>  PME redist. X/F8 358822  1446552.180   543850.913.1
>  PME spread/gather  8 358822   820940.059   308643.5 7.5
>  PME 3D-FFT 8 358822  6426689.995  2416201.058.4
>  PME solve  8 179411 5033.523 1892.4 0.0
> ---
>
> Parallel run - timing based on wallclock.
>
>NODE (s)   Real (s)  (%)
>Time: 517026.991 517026.991100.0
>   5d23h37:06
>(Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
> Performance:  9.634506.361  0.060400.250
> Finished mdrun on node 0 Tue Feb 25 13:34:48 2014
> --
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Re: [gmx-users] please guide me through the confusing gromacs results!!!

[Justin Lemkul]

On 2/26/14, 4:31 AM, delara aghaie wrote:

Dear Gromacs users,
we want to simulateHSA protein using8 processors. Usually with our available 
system 10ns simulation on 8 processors lasts 2-3 days.
This time we submitted 10 ns simulation, after almost 6 days it has finished 
but when we look at md.log file, only 179411 steps has been completed and all 
the averages are over this time, although we have submitted the run 500 
steps=10ns
1) First I want to know how the log file shows the end of simulation, although 
only 0.35 ns of simulation is done and if we draw RDF the time again shows 
completing of 0.35 ns.
you can see the ending part of log file below:
2) the second point is that the average load imbalance is shown as 110.3% while 
for previous runs we had this as 3-4 %.
what can be the reason for this high load imbalance?
and is this responsible for the lower simulation efficiency and higher time?


Something is unhealthy with the nodes you ran on; either they had other jobs 
running that competed with yours or something is simply wrong with one or more 
of them.



and the most important that why the log file is written in the way that the 
simulation has been completed while only 0.3 ns has passes?


Something caused the run to end, and when that happens, mdrun writes the 
statistics to the .log file.  Presumably you hit a wallclock limit or something 
that told mdrun to stop.


-Justin


Thanks for your time
**
  D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

  av. #atoms communicated per step for force:  2 x 97992.1
  av. #atoms communicated per step for LINCS:  2 x 2373.8

  Average load imbalance: 110.3 %
  Part of the total run time spent waiting due to load imbalance: 1.4 %


  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

  Computing: Nodes Number G-CyclesSeconds %
---
  Domain decomp. 8  35882   556174.638   209101.4 5.1
  DD comm. load  8359  235.791   88.6 0.0
  Comm. coord.   8 179411   407595.614   153241.1 3.7
  Neighbor search8  3588339333.69814788.0 0.4
  Force  8 179411   205203.39377149.0 1.9
  Wait + Comm. F 8 179411   471040.171   177093.9 4.3
  PME mesh   8 179411  8699277.459  3270611.079.1
  Write traj.875215563.463 5851.3 0.1
  Update 8 17941112991.140 4884.2 0.1
  Constraints8 179411   438837.169   164986.8 4.0
  Comm. energies 8  35884   149298.11156130.6 1.4
  Rest   86090.776 2289.9 0.1
---
  Total  811001641.424  4136215.9   100.0
---
---
  PME redist. X/F8 358822  1446552.180   543850.913.1
  PME spread/gather  8 358822   820940.059   308643.5 7.5
  PME 3D-FFT 8 358822  6426689.995  2416201.058.4
  PME solve  8 179411 5033.523 1892.4 0.0
---

 Parallel run - timing based on wallclock.

NODE (s)   Real (s)  (%)
Time: 517026.991 517026.991100.0
   5d23h37:06
(Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:  9.634506.361  0.060400.250
Finished mdrun on node 0 Tue Feb 25 13:34:48 2014



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] difference in potenital energy on desktop and server run

[Justin Lemkul]

On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:

Dear allI performed MD simulation of lipid bilayer on my desktop it is giving
correct results and negative potential energy (~ -10^5) but when I ran the
same simulation on a server using multi thread (-nt 8), It is giving
positive potential energy (~ 10^5). Initially I thought it might be problem
with mpi to check this I ran simulation on cluster with single thread but
still potential energy is positive.Any help would be appreciated



If the potential energy was that high, I would suspect the system crashed - did 
it?  What were you running, EM or MD?  If the latter, did you provide the 
correct, energy-minimized structure to grompp when creating the .tpr file for 
the run?  Detailed commands and actual output would be useful here, otherwise 
it's all guesswork.


Also, what version of Gromacs are you using?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] C-terminus residue name in Gromos43a1

[Justin Lemkul]

On 2/26/14, 4:08 AM, Francesca Vitalini wrote:

Dear Justin


2014-02-25 19:07 GMT+01:00 Justin Lemkul :




On 2/25/14, 12:56 PM, Francesca Vitalini wrote:


Dear Justin,

Thanks for your answer.
However I noticed that I had made a mistake and there is no definition of
NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at.

So defining a new residue-type in the rtp file is not as trivial as I had
hoped.
I followed the instructions given on the GROMACS wab page
http://www.gromacs.org/Documentation/How-tos/Adding_
a_Residue_to_a_Force_Field

and copied the gromos43a1.ff folder and the residuetypes.dat file in my
local directory.
I have added the following definition of NAC to the
gromos43a1.ff/aminoacids.rtp file

[ NAC ]
   [ atoms ]
  N N-0.28000 0
  H H 0.28000 0
 CA   CH3 0.0 0
   [ bonds ]
  NCAgb_20
  N Hgb_2



You're missing a bond here, from N to -C.



I hadn't add that as all the other residue types also don't have it
defined. It seems to me that the bond is defined as C to N+ not the other
way round. In this case however I have no N+ and the hydrogens are not
defined, so how can I properly define that bond?

I also tried to define the bond N to -C as gb_9 (ie the bond type of C to
N+) but it leads to the exact same error message.



Ah, true, this isn't necessary.





[ angles ]

;  aiajak   gromos type
 -C N H ga_31
  H NCA ga_17
 -C NCA ga_30
   [ impropers ]
;  aiajakal   gromos type
  N-CCA H gi_1
   [ dihedrals ]
;  aiajakal   gromos type
-CA-C NCA gd_4

and then tried again the pdb2gmx command as following and obtained this
error
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors


Evidently I have not defined correctly my NAC residue. However, I am not
sure of how to correctly define the bonds in this specific case. Could you
possibly identify the error and/or point me where to find detailed
information? I have already looked at the manual but haven't been able to
come up with successful definition.



You need to use pdb2gmx -ter and select "None" for the C-terminus,
otherwise pdb2gmx tries to build a carboxylate.  When it can't find the
atoms it needs to do this, it fails.



I do use the -ter "None" option for both termini and the error is still
present. What I find interesting is this part of the pdb2gmx output

Select start terminus type for ACE-1
  0: NH3+
  1: NH2
  2: None
2
Start terminus ACE-1: None
Select end terminus type for ACE-1
  0: COO-
  1: COOH
  2: None
2
End terminus ACE-1: None


where it looks like that ACE is the end terminus, not NAC, despite my pdb
looks like the following. Any suggestions?



What is residue 2?  Is it anything non-standard?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] please guide me through the confusing gromacs results!!!

[delara aghaie]

Dear Gromacs users,
we want to simulateHSA protein using8 processors. Usually with our available 
system 10ns simulation on 8 processors lasts 2-3 days.
This time we submitted 10 ns simulation, after almost 6 days it has finished 
but when we look at md.log file, only 179411 steps has been completed and all 
the averages are over this time, although we have submitted the run 500 
steps=10ns
1) First I want to know how the log file shows the end of simulation, although 
only 0.35 ns of simulation is done and if we draw RDF the time again shows 
completing of 0.35 ns.
you can see the ending part of log file below:
2) the second point is that the average load imbalance is shown as 110.3% while 
for previous runs we had this as 3-4 %.
what can be the reason for this high load imbalance? 
and is this responsible for the lower simulation efficiency and higher time? 
and the most important that why the log file is written in the way that the 
simulation has been completed while only 0.3 ns has passes?
Thanks for your time
**
 D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 97992.1
 av. #atoms communicated per step for LINCS:  2 x 2373.8

 Average load imbalance: 110.3 %
 Part of the total run time spent waiting due to load imbalance: 1.4 %


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing:         Nodes     Number     G-Cycles    Seconds     %
---
 Domain decomp.         8      35882   556174.638   209101.4     5.1
 DD comm. load          8        359      235.791       88.6     0.0
 Comm. coord.           8     179411   407595.614   153241.1     3.7
 Neighbor search        8      35883    39333.698    14788.0     0.4
 Force                  8     179411   205203.393    77149.0     1.9
 Wait + Comm. F         8     179411   471040.171   177093.9     4.3
 PME mesh               8     179411  8699277.459  3270611.0    79.1
 Write traj.            8        752    15563.463     5851.3     0.1
 Update                 8     179411    12991.140     4884.2     0.1
 Constraints            8     179411   438837.169   164986.8     4.0
 Comm. energies         8      35884   149298.111    56130.6     1.4
 Rest                   8                6090.776     2289.9     0.1
---
 Total                  8            11001641.424  4136215.9   100.0
---
---
 PME redist. X/F        8     358822  1446552.180   543850.9    13.1
 PME spread/gather      8     358822   820940.059   308643.5     7.5
 PME 3D-FFT             8     358822  6426689.995  2416201.0    58.4
 PME solve              8     179411     5033.523     1892.4     0.0
---

        Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time: 517026.991 517026.991    100.0
                      5d23h37:06
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      9.634    506.361      0.060    400.250
Finished mdrun on node 0 Tue Feb 25 13:34:48 2014
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Re: [gmx-users] User-defined Potentials in Gromacs

[Dr. Vitaly Chaban]

>> I have looked up "tabulated potential" in the manual and also the suggested
>> document, neither of them actually helps the situation.

Why do they not?


Dr. Vitaly V. Chaban
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Re: [gmx-users] C-terminus residue name in Gromos43a1

[Francesca Vitalini]

Dear Justin


2014-02-25 19:07 GMT+01:00 Justin Lemkul :

>
>
> On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
>
>> Dear Justin,
>>
>> Thanks for your answer.
>> However I noticed that I had made a mistake and there is no definition of
>> NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at.
>>
>> So defining a new residue-type in the rtp file is not as trivial as I had
>> hoped.
>> I followed the instructions given on the GROMACS wab page
>> http://www.gromacs.org/Documentation/How-tos/Adding_
>> a_Residue_to_a_Force_Field
>>
>> and copied the gromos43a1.ff folder and the residuetypes.dat file in my
>> local directory.
>> I have added the following definition of NAC to the
>> gromos43a1.ff/aminoacids.rtp file
>>
>> [ NAC ]
>>   [ atoms ]
>>  N N-0.28000 0
>>  H H 0.28000 0
>> CA   CH3 0.0 0
>>   [ bonds ]
>>  NCAgb_20
>>  N Hgb_2
>>
>
> You're missing a bond here, from N to -C.


I hadn't add that as all the other residue types also don't have it
defined. It seems to me that the bond is defined as C to N+ not the other
way round. In this case however I have no N+ and the hydrogens are not
defined, so how can I properly define that bond?

I also tried to define the bond N to -C as gb_9 (ie the bond type of C to
N+) but it leads to the exact same error message.


>
>[ angles ]
>> ;  aiajak   gromos type
>> -C N H ga_31
>>  H NCA ga_17
>> -C NCA ga_30
>>   [ impropers ]
>> ;  aiajakal   gromos type
>>  N-CCA H gi_1
>>   [ dihedrals ]
>> ;  aiajakal   gromos type
>>-CA-C NCA gd_4
>>
>> and then tried again the pdb2gmx command as following and obtained this
>> error
>> Fatal error:
>> There is a dangling bond at at least one of the terminal ends. Select a
>> proper terminal entry.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> Evidently I have not defined correctly my NAC residue. However, I am not
>> sure of how to correctly define the bonds in this specific case. Could you
>> possibly identify the error and/or point me where to find detailed
>> information? I have already looked at the manual but haven't been able to
>> come up with successful definition.
>>
>>
> You need to use pdb2gmx -ter and select "None" for the C-terminus,
> otherwise pdb2gmx tries to build a carboxylate.  When it can't find the
> atoms it needs to do this, it fails.
>

I do use the -ter "None" option for both termini and the error is still
present. What I find interesting is this part of the pdb2gmx output

Select start terminus type for ACE-1
 0: NH3+
 1: NH2
 2: None
2
Start terminus ACE-1: None
Select end terminus type for ACE-1
 0: COO-
 1: COOH
 2: None
2
End terminus ACE-1: None


where it looks like that ACE is the end terminus, not NAC, despite my pdb
looks like the following. Any suggestions?

Thanks

Francesca

TITLEACETYL-ALANINE-METHYLAMIDE
REMARK   GENERATED BY CUTTING OUT RESIDUE 14 TO 16 FROM FROM 2KSZ.PDB SEQ 1
MODEL1
ATOM1   1HH3  ACE A  1   9.955  -1.448  -7.763  1.00
0.00   H
ATOM2   CA   ACE A  1  10.830  -2.612  -7.822  1.00  0.00
C
ATOM3   C ACE A  1  10.355  -3.683  -6.846  1.00
0.00   C
ATOM4   O ACE A  1  10.264  -4.861  -7.196  1.00
0.00   O
ATOM5   2HH3  ACE A  1  12.264  -2.204  -7.476  1.00
0.00   H
ATOM6   3HH3  ACE A  1  10.814  -3.010  -8.826  1.00
0.00   H
ATOM7   N ALA A  2  10.042  -3.264  -5.625  1.00
0.00   N
ATOM8   CAALA A  2   9.563  -4.193  -4.609  1.00
0.00   C
ATOM9   C ALA A  2   8.170  -4.706  -4.969  1.00
0.00   C
ATOM10  O ALA A  2   7.806  -5.832  -4.630  1.00
0.00   O
ATOM11  CBALA A  2   9.507  -3.492  -3.251  1.00
0.00   C
ATOM12  H ALA A  2  10.127  -2.310  -5.408  1.00
0.00   H
ATOM13  HAALA A  2  10.248  -5.025  -4.538  1.00
0.00   H
ATOM14  HB1   ALA A  2   9.115  -4.175  -2.509  1.00
0.00   H
ATOM15  HB2   ALA A  2   8.867  -2.625  -3.317  1.00
0.00   H
ATOM16  HB3   ALA A  2  10.502  -3.185  -2.963  1.00
0.00   H
ATOM17  N NAC A  3   7.398  -3.868  -5.656  1.00
0.00   N
ATOM18  CANAC A  3   6.046  -4.242  -6.057  1.00
0.00   C
ATOM19  1HH3  NAC A  3   6.078  -5.329  -7.127  1.00
0.00   H
ATOM20  2HH3  NAC A  3   5.308  -3.015  -6.599  1.00
0.00   H
ATOM21  H NAC A  3   7.743  -2.984  -5.899  1.00
0.00   H
ATOM22  3HH3  NAC A  3   5.512  -4.613  -5.197  1.00
0.00   H
~

~




> -Justin
>
>
> --
>