[gmx-users] Re: amber force field in Gromacs
Hi Alan,
Thank you for all your efforts. This is getting strange, I tried
following your procedure below but is still does not work for me:
step 3500, will finish Fri Dec 4 09:56:51 2009Warning: 1-4 interaction
between 6 and 10 at distance 1.454 which is larger than the 1-4 table
size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
kind regards,
Servaas
> Message: 1
> Date: Thu, 3 Dec 2009 11:23:14 +
> From: Alan
> Subject: [gmx-users] Re: amber force field in Gromacs
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Servaas,
>
> Tested again in 'vacuum' and I saw no problems. Here goes what I did:
>
>
> #--
> cat << EOF >| leap.in
> verbosity 1
> source leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> saveamberparm ad da_amber.top da_amber.crd
> savepdb ad DA.pdb
> quit
> EOF
> tleap -f leap.in >| leap.out
>
> acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and
> md.mdp
>
> cat << EOF >| md.mdp
> cpp = /usr/bin/cpp
> define = ;-DFLEXIBLE
> integrator = md
> nsteps = 25
> constraints = none
> emtol= 1000.0
> emstep = 0.01
> comm_mode= angular
> ns_type = simple
> nstlist = 0
> rlist= 0
> rcoulomb = 0
> rvdw = 0
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 100
> pbc = no
> EOF
>
> editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro
>
> #Single precision
> grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun -v -deffnm em
>
> grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun -v -deffnm md
>
> vmd md.gro md.trr
> #--
>
> As you may suspect from the beginning it may be something in your mdp file.
> Case the example above works, I would suggest you to try the mdp for solvent
> box I sent before in a long simulation.
>
> Good luck.
>
> Regards,
>
> Alan
>
> On Wed, Dec 2, 2009 at 11:10, Alan wrote:
>
> > Dear Servaas,
> >
> > In tleap did you really did:
> >
> > TLEAP
> > tleap -f leaprc.ff99SB
> > ad = sequence { DA5 DA DA3 }
> > saveamberparm da da_amber.top da_amber.crd
> >
> >
> > If so, it's wrong, it should be:
> >
> > saveamberparm ad da_amber.top da_amber.crd
> >^^^
> > and not 'da'
> >
> > Besides, I tried to reproduce what you did using what I think would be
> > fine and... everything went fine! Energies after minimisation in
> > single and double were almost identical and trajectories diverted
> > normally.
> >
> > Please check what I did.
> >
> > # begin commands
> >
> > cat << EOF >| em.mdp
> > define = -DFLEXIBLE
> > integrator = cg ; steep
> > nsteps = 200
> > constraints = none
> > emtol= 1000.0
> > nstcgsteep = 10 ; do a steep every 10 steps of cg
> > emstep = 0.01 ; used with steep
> > nstcomm = 1
> > coulombtype = PME
> > ns_type = grid
> > rlist= 1.0
> > rcoulomb = 1.0
> > rvdw = 1.4
> > Tcoupl = no
> > Pcoupl = no
> > gen_vel = no
> > nstxout = 0 ; write coords every # step
> > optimize_fft = yes
> > EOF
> >
> >
> > cat << EOF >| md.mdp
> > integrator = md
> > nsteps = 1000
> > dt = 0.002
> > constraints = all-bonds
> > nstcomm = 1
> > ns_type = grid
> > rlist= 1.2
> > rcoulomb = 1.1
> > rvdw = 1.0
> > vdwtype = shift
> > rvdw-switch = 0.9
> > coulombtype = PME-Switch
> > Tcoupl = v-rescale
> > tau_t
[gmx-users] Re: amber force field in Gromacs
Dear Servaas,
Tested again in 'vacuum' and I saw no problems. Here goes what I did:
#--
cat << EOF >| leap.in
verbosity 1
source leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm ad da_amber.top da_amber.crd
savepdb ad DA.pdb
quit
EOF
tleap -f leap.in >| leap.out
acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and
md.mdp
cat << EOF >| md.mdp
cpp = /usr/bin/cpp
define = ;-DFLEXIBLE
integrator = md
nsteps = 25
constraints = none
emtol= 1000.0
emstep = 0.01
comm_mode= angular
ns_type = simple
nstlist = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 100
pbc = no
EOF
editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro
#Single precision
grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
mdrun -v -deffnm em
grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun -v -deffnm md
vmd md.gro md.trr
#--
As you may suspect from the beginning it may be something in your mdp file.
Case the example above works, I would suggest you to try the mdp for solvent
box I sent before in a long simulation.
Good luck.
Regards,
Alan
On Wed, Dec 2, 2009 at 11:10, Alan wrote:
> Dear Servaas,
>
> In tleap did you really did:
>
> TLEAP
> tleap -f leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> saveamberparm da da_amber.top da_amber.crd
>
>
> If so, it's wrong, it should be:
>
> saveamberparm ad da_amber.top da_amber.crd
>^^^
> and not 'da'
>
> Besides, I tried to reproduce what you did using what I think would be
> fine and... everything went fine! Energies after minimisation in
> single and double were almost identical and trajectories diverted
> normally.
>
> Please check what I did.
>
> # begin commands
>
> cat << EOF >| em.mdp
> define = -DFLEXIBLE
> integrator = cg ; steep
> nsteps = 200
> constraints = none
> emtol= 1000.0
> nstcgsteep = 10 ; do a steep every 10 steps of cg
> emstep = 0.01 ; used with steep
> nstcomm = 1
> coulombtype = PME
> ns_type = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| md.mdp
> integrator = md
> nsteps = 1000
> dt = 0.002
> constraints = all-bonds
> nstcomm = 1
> ns_type = grid
> rlist= 1.2
> rcoulomb = 1.1
> rvdw = 1.0
> vdwtype = shift
> rvdw-switch = 0.9
> coulombtype = PME-Switch
> Tcoupl = v-rescale
> tau_t= 0.1 0.1
> tc-grps = protein non-protein
> ref_t= 300 300
> Pcoupl = parrinello-rahman
> Pcoupltype = isotropic
> tau_p= 0.5
> compressibility = 4.5e-5
> ref_p= 1.0
> gen_vel = yes
> nstxout = 2 ; write coords every # step
> lincs-iter = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| leap.in
> verbosity 1
> source leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> solvatebox ad TIP3PBOX 10.0
> addions ad Na+ 5
> addions ad Cl- 3
> saveamberparm ad da_amber.top da_amber.crd
> savepdb ad DA.pdb
> quit
> EOF
> tleap -f leap.in >| leap.out
>
> acpypi -x da_amber.crd -p da_amber.top -d
>
> #Single precision
> grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.2280516e+04
> #Maximum force = 7.5868494e+02 on atom 98
> #Norm of force = 1.0447179e+02
>
> grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun -v -deffnm md
>
> #Double precision
> grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun_d -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.22813514022256e+04
> #Maximum force = 7.58238100790309e+02 on atom 98
> #Norm of force = 1.04358667410458e+02
>
> grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun_d -v -deffnm md
>
> # end commands
>
> Reg
[gmx-users] Re: amber force field in Gromacs
> Dear Servaas,
>
> In tleap did you really did:
>
> TLEAP
> tleap -f leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> saveamberparm da da_amber.top da_amber.crd
>
>
> If so, it's wrong, it should be:
>
> saveamberparm ad da_amber.top da_amber.crd
> ^^^
> and not 'da'
Yes of course just a typo here
>
> Besides, I tried to reproduce what you did using what I think would be
> fine and... everything went fine! Energies after minimisation in
> single and double were almost identical and trajectories diverted
> normally.
Did you also try running it in vacuum? In solvent the problems occur
only after a large number of steps. In vacuum they occur very fast. I
know vacuum is not the way to go, but I consider it as quick test, if a
short simulation in vacuum gives strange things it is an indication of a
problem with the parameters (force fiels or others...). Amber doesn't
give me any problems in vacuum, this gives me an indication that the
vacuum is not the problem here.
>
> Please check what I did.
>
> # begin commands
>
> cat << EOF >| em.mdp
> define = -DFLEXIBLE
> integrator = cg ; steep
> nsteps = 200
> constraints = none
> emtol= 1000.0
> nstcgsteep = 10 ; do a steep every 10 steps of cg
> emstep = 0.01 ; used with steep
> nstcomm = 1
> coulombtype = PME
> ns_type = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| md.mdp
> integrator = md
> nsteps = 1000
> dt = 0.002
> constraints = all-bonds
> nstcomm = 1
> ns_type = grid
> rlist= 1.2
> rcoulomb = 1.1
> rvdw = 1.0
> vdwtype = shift
> rvdw-switch = 0.9
> coulombtype = PME-Switch
> Tcoupl = v-rescale
> tau_t= 0.1 0.1
> tc-grps = protein non-protein
> ref_t= 300 300
> Pcoupl = parrinello-rahman
> Pcoupltype = isotropic
> tau_p= 0.5
> compressibility = 4.5e-5
> ref_p= 1.0
> gen_vel = yes
> nstxout = 2 ; write coords every # step
> lincs-iter = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| leap.in
> verbosity 1
> source leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> solvatebox ad TIP3PBOX 10.0
> addions ad Na+ 5
> addions ad Cl- 3
> saveamberparm ad da_amber.top da_amber.crd
> savepdb ad DA.pdb
> quit
> EOF
> tleap -f leap.in >| leap.out
>
> acpypi -x da_amber.crd -p da_amber.top -d
>
> #Single precision
> grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.2280516e+04
> #Maximum force = 7.5868494e+02 on atom 98
> #Norm of force = 1.0447179e+02
>
> grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun -v -deffnm md
>
> #Double precision
> grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun_d -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.22813514022256e+04
> #Maximum force = 7.58238100790309e+02 on atom 98
> #Norm of force = 1.04358667410458e+02
>
> grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun_d -v -deffnm md
>
> # end commands
>
> Regards,
>
> Alan
--
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[gmx-users] Re: amber force field in Gromacs
Dear Servaas,
In tleap did you really did:
TLEAP
tleap -f leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm da da_amber.top da_amber.crd
If so, it's wrong, it should be:
saveamberparm ad da_amber.top da_amber.crd
^^^
and not 'da'
Besides, I tried to reproduce what you did using what I think would be
fine and... everything went fine! Energies after minimisation in
single and double were almost identical and trajectories diverted
normally.
Please check what I did.
# begin commands
cat << EOF >| em.mdp
define = -DFLEXIBLE
integrator = cg ; steep
nsteps = 200
constraints = none
emtol= 1000.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
coulombtype = PME
ns_type = grid
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes
EOF
cat << EOF >| md.mdp
integrator = md
nsteps = 1000
dt = 0.002
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist= 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t= 0.1 0.1
tc-grps = protein non-protein
ref_t= 300 300
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p= 0.5
compressibility = 4.5e-5
ref_p= 1.0
gen_vel = yes
nstxout = 2 ; write coords every # step
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
EOF
cat << EOF >| leap.in
verbosity 1
source leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
solvatebox ad TIP3PBOX 10.0
addions ad Na+ 5
addions ad Cl- 3
saveamberparm ad da_amber.top da_amber.crd
savepdb ad DA.pdb
quit
EOF
tleap -f leap.in >| leap.out
acpypi -x da_amber.crd -p da_amber.top -d
#Single precision
grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
mdrun -v -deffnm em
#Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
#Potential Energy = -6.2280516e+04
#Maximum force = 7.5868494e+02 on atom 98
#Norm of force = 1.0447179e+02
grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun -v -deffnm md
#Double precision
grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
mdrun_d -v -deffnm em
#Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
#Potential Energy = -6.22813514022256e+04
#Maximum force = 7.58238100790309e+02 on atom 98
#Norm of force = 1.04358667410458e+02
grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun_d -v -deffnm md
# end commands
Regards,
Alan
On Tue, Dec 1, 2009 at 13:56, Alan wrote:
> Dear Servaas,
>
> I've been following your thread. I am the developer of acpypi and
> thanks for giving a try.
>
> So, as you may already know, you are trying acpypi as amb2gmx.pl so
> far, but you also seemed to have read acpypi wikis and realise that
> acpypi can help you to generate the whole topology for a ligand.
>
> However, AFAIU you have only regular NA and not modified ones neither
> ligands, right? But then why are you using RED?
>
> I understand your approach about using tleap to create your whole
> system and then convert it to GMX. It should work at first but it is
> clearly not as you reported.
>
> So, here goes some of my recommendations:
>
> 1) GMX is vacuum is unrealistic and prone for errors. There's no GB
> implementation as far as I know.
>
> 2) Have you try to use pdb2gmx to generate your files from your pdb
> directly to GMX?
>
> 3) When you say that gmx double precision works, is your system in
> vacuum or with solvent?
>
> 4) if using tleap, create your system with solvent and ions and then
> use acpypi to convert to gmx.
>
> The use of amb2gmx or acpypi is to give you a system to be run
> immediately in gromacs doing just a grompp and mdrun. Using editconf
> will change the parameters of your box and it may have serious
> implications besides that in amber we don't have dodecahedron, so if
> doing what you're doing then you're not replicating the conditions you
> have in amber with those in gmx (although it puzzles me that gmx
> double works, with the commands you gave in gmx?).
>
> I would ask you to give more details and even a detailed step by step
> of commands of what you're doing including tleap.
>
> Regards,
> Alan
>
>
>
> On Tue, Dec 1, 2009 at 11:00, wrote
[gmx-users] Re: amber force field in Gromacs
Dear Servaas, I've been following your thread. I am the developer of acpypi and thanks for giving a try. So, as you may already know, you are trying acpypi as amb2gmx.pl so far, but you also seemed to have read acpypi wikis and realise that acpypi can help you to generate the whole topology for a ligand. However, AFAIU you have only regular NA and not modified ones neither ligands, right? But then why are you using RED? I understand your approach about using tleap to create your whole system and then convert it to GMX. It should work at first but it is clearly not as you reported. So, here goes some of my recommendations: 1) GMX is vacuum is unrealistic and prone for errors. There's no GB implementation as far as I know. 2) Have you try to use pdb2gmx to generate your files from your pdb directly to GMX? 3) When you say that gmx double precision works, is your system in vacuum or with solvent? 4) if using tleap, create your system with solvent and ions and then use acpypi to convert to gmx. The use of amb2gmx or acpypi is to give you a system to be run immediately in gromacs doing just a grompp and mdrun. Using editconf will change the parameters of your box and it may have serious implications besides that in amber we don't have dodecahedron, so if doing what you're doing then you're not replicating the conditions you have in amber with those in gmx (although it puzzles me that gmx double works, with the commands you gave in gmx?). I would ask you to give more details and even a detailed step by step of commands of what you're doing including tleap. Regards, Alan On Tue, Dec 1, 2009 at 11:00, wrote: > > Thanks for your suggestion, I tried without success and I also tried > shake. But this is also rather fighting the symptoms than the cause... > And amber simulations in vacuum do work fine... My personal guess was > that another parameter in my mdp file was not compatible with the amber > force field, but I could not figure out which one. I also tried > different settings, e.g. the one I found on the acpypi wiki. > -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: amber force field in Gromacs
> -- > > Message: 4 > Date: Tue, 01 Dec 2009 10:51:17 +0100 > From: Erik Marklund > Subject: Re: [gmx-users] Re: amber force field in Gromacs > To: Discussion list for GROMACS users > Message-ID: <4b14e715.3030...@xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > Vacuum simulations are trickier than in solvent, more often causing > lincs errors. Have you tried playing around with lincs order and lincs iter? > > /Erik Thanks for your suggestion, I tried without success and I also tried shake. But this is also rather fighting the symptoms than the cause... And amber simulations in vacuum do work fine... My personal guess was that another parameter in my mdp file was not compatible with the amber force field, but I could not figure out which one. I also tried different settings, e.g. the one I found on the acpypi wiki. > > servaas skrev: > >> Message: 6 > >> Date: Tue, 01 Dec 2009 07:38:29 +1100 > >> From: Mark Abraham > >> Subject: Re: [gmx-users] amber force field in Gromacs > >> To: Discussion list for GROMACS users > >> Message-ID: <4b142d45.5050...@anu.edu.au> > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >> > >> servaas wrote: > >> > >>> Hello, > >>> > >>> I tried using the amber force field in GROMACS. I proceeded as follows: > >>> Determined my parameters with RED/ANTECHAMBER/tleap converted them with > >>> amb2gmx.pl > >>> (or with acpypi, problem is the same) to gromacs coordinate and topology > >>> files. It concerns a modified nucleotide. I minimized with steepest > >>> descent, everything was fine. > >>> When I tried running a simulation in single precision with this .mdp file > >>> (only nucleotide without solvent): > >>> > >>> integrator = md > >>> > >>> dt = 0.002 > >>> nsteps = 25 > >>> nstcomm = 1 > >>> > >>> ;output > >>> nstxout = 1 > >>> nstvout = 1 > >>> nstfout = 0 > >>> nstlog= 500 > >>> nstenergy = 1 > >>> > >>> nstlist = 10 > >>> ns_type = grid > >>> rlist= 1.2 > >>> coulombtype = PME > >>> rcoulomb = 1.2 > >>> vdwtype = cut-off > >>> rvdw = 1.2 > >>> > >>> fourierspacing = 0.12 > >>> pme_order= 4 > >>> ewald_rtol = 1e-5 > >>> > >>> ;constraints > >>> constraints = all-bonds > >>> > >>> > >>> ; temperature coupling is on > >>> Tcoupl = v-rescale > >>> tau_t = 0.1 > >>> tc-grps = system > >>> ref_t = 300 > >>> > >>> pcoupl = no > >>> > >>> I get LINCS errors and eventually a crash. Now I tried running the same > >>> simulation with the same force field parameters in amber and everything > >>> was fine. > >>> I also ran the calculation in GROMACS with double precision here again > >>> everything was fine... I also tried running a small nucleic acid fragment > >>> (so no modified parameters here) > >>> that I created in tleap and converted to GROMACS again this crashes with > >>> lincs errors in GROMACS. When I look at the trajectories it is the O4' of > >>> the ribose who clashes with the O3'. > >>> > >>> The fact that I still get this problem with non modified amber parameters > >>> makes me thing there is something wrong with my .mdp file to run with > >>> amber FF, any suggestions? > >>> Strange also that double precision seems to work just fine > >>> > >> When switching precision, are the starting configurations different? > >> What are the actual command lines in your procedures? > >> > > It is the exact same structure, when I look at the trajectory I see the > > O3'-H rotate towards the O4' in the single precision trajectory they > > come too close and clash. In the double precision trajectory the O3'-H > > also rotates towards O4' but they do not come so close... > > > > I did not include the command lines for amber and RED, please let me > > know if they are relevant t
Re: [gmx-users] Re: amber force field in Gromacs
Hi, Vacuum simulations are trickier than in solvent, more often causing lincs errors. Have you tried playing around with lincs order and lincs iter? /Erik servaas skrev: Message: 6 Date: Tue, 01 Dec 2009 07:38:29 +1100 From: Mark Abraham Subject: Re: [gmx-users] amber force field in Gromacs To: Discussion list for GROMACS users Message-ID: <4b142d45.5050...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas wrote: Hello, I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine. When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent): integrator = md dt = 0.002 nsteps = 25 nstcomm = 1 ;output nstxout = 1 nstvout = 1 nstfout = 0 nstlog= 500 nstenergy = 1 nstlist = 10 ns_type = grid rlist= 1.2 coulombtype = PME rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.2 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 ;constraints constraints = all-bonds ; temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = system ref_t = 300 pcoupl = no I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine. I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here) that I created in tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions? Strange also that double precision seems to work just fine When switching precision, are the starting configurations different? What are the actual command lines in your procedures? It is the exact same structure, when I look at the trajectory I see the O3'-H rotate towards the O4' in the single precision trajectory they come too close and clash. In the double precision trajectory the O3'-H also rotates towards O4' but they do not come so close... I did not include the command lines for amber and RED, please let me know if they are relevant to you. So first I use RED to determine the charges of different fragments of my molecule. The result are several mol2 files, I use tleap to combine this mol2 file with parts of existing amber fragments. I save an amber top and amber crd file. I convert this with amb2gmx or with acpypi (tried both same result in the simulation). ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro or python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro Then I add a box in gromacs: editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro I run a minimization: grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr mdrun -deffnm em (Also tried putting a position restraint step in between, did not resolve the problem) grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr mdrun -deffnm md Extra remarks: Simulation in vacuum is not realistic and the FF is not made for this but I also tried running it with counter ions and water, same result. In amber I can simulate the exact same molecule in vacuum, with same parameters without any problems. The exact same problem occurs if I start with a small natural nucleic acid sequence (3*DA), so 100% amber FF parameters (but created in amber and converted with amb2gmx.pl). Kind regards, Servaas Mark -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 67, Issue 152 ** -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gro
[gmx-users] Re: amber force field in Gromacs
> > Message: 6 > Date: Tue, 01 Dec 2009 07:38:29 +1100 > From: Mark Abraham > Subject: Re: [gmx-users] amber force field in Gromacs > To: Discussion list for GROMACS users > Message-ID: <4b142d45.5050...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > servaas wrote: > > Hello, > > > > I tried using the amber force field in GROMACS. I proceeded as follows: > > Determined my parameters with RED/ANTECHAMBER/tleap converted them with > > amb2gmx.pl > > (or with acpypi, problem is the same) to gromacs coordinate and topology > > files. It concerns a modified nucleotide. I minimized with steepest > > descent, everything was fine. > > When I tried running a simulation in single precision with this .mdp file > > (only nucleotide without solvent): > > > > integrator = md > > > > dt = 0.002 > > nsteps = 25 > > nstcomm = 1 > > > > ;output > > nstxout = 1 > > nstvout = 1 > > nstfout = 0 > > nstlog= 500 > > nstenergy = 1 > > > > nstlist = 10 > > ns_type = grid > > rlist= 1.2 > > coulombtype = PME > > rcoulomb = 1.2 > > vdwtype = cut-off > > rvdw = 1.2 > > > > fourierspacing = 0.12 > > pme_order= 4 > > ewald_rtol = 1e-5 > > > > ;constraints > > constraints = all-bonds > > > > > > ; temperature coupling is on > > Tcoupl = v-rescale > > tau_t = 0.1 > > tc-grps = system > > ref_t = 300 > > > > pcoupl = no > > > > I get LINCS errors and eventually a crash. Now I tried running the same > > simulation with the same force field parameters in amber and everything was > > fine. > > I also ran the calculation in GROMACS with double precision here again > > everything was fine... I also tried running a small nucleic acid fragment > > (so no modified parameters here) > > that I created in tleap and converted to GROMACS again this crashes with > > lincs errors in GROMACS. When I look at the trajectories it is the O4' of > > the ribose who clashes with the O3'. > > > > The fact that I still get this problem with non modified amber parameters > > makes me thing there is something wrong with my .mdp file to run with amber > > FF, any suggestions? > > Strange also that double precision seems to work just fine > > When switching precision, are the starting configurations different? > What are the actual command lines in your procedures? It is the exact same structure, when I look at the trajectory I see the O3'-H rotate towards the O4' in the single precision trajectory they come too close and clash. In the double precision trajectory the O3'-H also rotates towards O4' but they do not come so close... I did not include the command lines for amber and RED, please let me know if they are relevant to you. So first I use RED to determine the charges of different fragments of my molecule. The result are several mol2 files, I use tleap to combine this mol2 file with parts of existing amber fragments. I save an amber top and amber crd file. I convert this with amb2gmx or with acpypi (tried both same result in the simulation). ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro or python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro Then I add a box in gromacs: editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro I run a minimization: grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr mdrun -deffnm em (Also tried putting a position restraint step in between, did not resolve the problem) grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr mdrun -deffnm md Extra remarks: Simulation in vacuum is not realistic and the FF is not made for this but I also tried running it with counter ions and water, same result. In amber I can simulate the exact same molecule in vacuum, with same parameters without any problems. The exact same problem occurs if I start with a small natural nucleic acid sequence (3*DA), so 100% amber FF parameters (but created in amber and converted with amb2gmx.pl). Kind regards, Servaas > > Mark > > > -- > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 67, Issue 152 > ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: amber force field in gromacs
Dear Leila, Consider reading all about ACPYPI at acpypi.googlecode.com, specially the wiki pages. Although you may not be interested in topology generation for ligands, there's there important information about how to run amber force fields in Gromacs environment. And review carefully your ffamber installation. It looks I had some similar issues in the past and although I never figured out what was the cause, a simply careful reinstallation of ffamber solved the problem. And if using amber force field, consider registering yourself at amber mailing list (ambermd.org). I am suggesting that because as far as I know from literature amber99sb is the most advanced force field from amber, yet the year, but read: Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. Compar- ison of multiple amber force fields and development of improved protein backbone parameters. Proteins- Structure Function and Bioinformatics 65, 3 (NOV 15 2006), 712–725. However, I understand you want to do nucleic acids simulation rather than proteins, so milage here is low and for that I suggested also the amber mailing list. I hope it may helps. Alan On Sat, Nov 21, 2009 at 11:00, wrote: > Send gmx-users mailing list submissions to > dear Mark > > your opinion is right [residue number 1 is NGLY in pdb file but residue > number 1 is GLY in warning]. > > howbeit, what work should I do? > -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
