[gmx-users] Re: acetonitrile from amber to gromacs

[Alan]

Dear Vedat,

Thank you very much indeed. Things only get better with constructive
feedbacks, either positive or negative.

Glad you're managing well your problem. However, as I see, your problem now
is in the tleap level.

So, are you in amber mailing list? If so I would suggest to post your
question there. If not, let me know and I try to post the question there
(you may want to consider joining it, very useful, even for those who uses
only ambertools).

However, at first, I would go ahead and neglect the error. In the end, if
you not happy, you can always adjust this particular parameter (in the itp
file), since in principle a triple bond would mean a stronger bond, so
implying in higher K-string constant. For how much to adjust? Well, you
cannot even ever say that you got is "correct"; all you can get is a better
or worse model and in the end it's up to you to set that.

Nevertheless, be sure that you have the right protonation state and try to
re-run your case putting CONECT info in the pdb just to check it.

I hope it helps.

Best,

Alan

On Fri, Jun 4, 2010 at 11:00,  wrote:

> hi alan and all others,
>
> i love it. i've probably never seen such a helpful and constuctive
> answer to a question asked over the gmx user mailing list. following
> your instructions was very informative on the one hand and provided the
> results that i needed on the other.
>
> slightly modifying the the ch3cn.frcmod and -.prep files from the
> manchester site in accordance with a newer solvent model for
> acetonitrile of the year 2007 and feeding tleap with that data resulted
> in a ch3cn.lib file and afterwards in ch3cn.prmtop and ch3cn.inpcrd
> which i could use as input for acpype in order to generate .gro and .itp
> files. perfect.
>
> almost perfect, because in tleap i was not able to add the YC-YN triple
> bond (with the "bond ..." command) without generating an error message
> when saving my parameter files ("saveAmberParm ..." command). see the
> following output:
>
>
> > bond C3N.1.C2 C3N.1.N1 "T"
> > saveAmberParm C3N ch3cn.prmtop ch3cn.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> !FATAL ERROR
> !FATAL:In file [unitio.c], line 1778
> !FATAL:Message: 1-4: cannot add bond 1 2
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
> !ABORTING.
>
> where could the "second" bond specification be, that avoids the
> specification of a triple bond "T"? there's no bonding information in
> the pdb file.
>
> a step earlier in tleap, i had to addAtomTypes YN and YC, however, there
> was no way to specify them with "sp" hybridization, but "sp2" resulting
> in two lines each containing a single bond between these two atoms
> within the "!entry.C3N.unit.connectivity table" section of the ch3cn.lib
> file (seems to be a double bond).
>
> is this issue negligible, since the force constants and equilibrium
> angles (180 degrees) are already describing the right molecule?
>
> vedat
>
>
>
>
> Alan schrieb:
> > Nice, glad you did progress. See below.
> >
> > On Thu, May 20, 2010 at 12:38,  > > wrote:
> >
> > thanks for your helpful hints. i updated acpype, created a pdb
> > file with
> > a single molecule and ran
> >
> > acpype -i ch3cn_210_single.pdb
> >
> > which generated an .itp and other interesting files. that's
> > nice. (remember, i want to use gromacs with amber99sb force field
> > and i
> > downloaded 3 files from the amber site: ch3cn_210.pdb,
> > frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)
> >
> > 1) the charges do not match the ones listed in the prep.ch3cn file.
> > shall i just change them by hand accordingly?
> >
> >
> > It doesn't match because it's using am1bcc, which was parametrised to
> > reproduce the RESP charges, but obviously (sqm is semi-empirical
> > method, not like gaussian)  it won't be accurate.
> >
> > However, you're right, if you have the RESP charges in prep.ch3cn just
> > copy them by hand accordingly.
> >
> > Or even better, if you want to learn more about the whole stuff,
> > double check if the parameters you got from the Manchester site are
> > OK, why not trying q4md-forcefieldtools.org/RED/
> > ? Once you got the charges (they
> > should be very close if not the same from  prep.ch3cn), you can use
> > acpype just to generate the topology by providing a c3n.MOL2 file with
> > the charges calculated by RED and then using "acpype -di c3n.mol2 -c
> > user".
> >
> >
> > 2) dummy atoms as listed in the prep.ch3cn are not present in the new
> > .itp file.
> >
> >
> > I guess you don't know how a prep file works, so
> > see http://ambermd.org/doc/prep.html.
> >
> >
> > 3) the force constants seem totally differ

Re: [gmx-users] Re: acetonitrile from amber to gromacs

[vedat durmaz]

hi alan and all others,

i love it. i've probably never seen such a helpful and constuctive
answer to a question asked over the gmx user mailing list. following
your instructions was very informative on the one hand and provided the
results that i needed on the other.

slightly modifying the the ch3cn.frcmod and -.prep files from the
manchester site in accordance with a newer solvent model for
acetonitrile of the year 2007 and feeding tleap with that data resulted
in a ch3cn.lib file and afterwards in ch3cn.prmtop and ch3cn.inpcrd
which i could use as input for acpype in order to generate .gro and .itp
files. perfect.

almost perfect, because in tleap i was not able to add the YC-YN triple
bond (with the "bond ..." command) without generating an error message
when saving my parameter files ("saveAmberParm ..." command). see the
following output:


> bond C3N.1.C2 C3N.1.N1 "T"
> saveAmberParm C3N ch3cn.prmtop ch3cn.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR
!FATAL:In file [unitio.c], line 1778
!FATAL:Message: 1-4: cannot add bond 1 2
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
!ABORTING.

where could the "second" bond specification be, that avoids the
specification of a triple bond "T"? there's no bonding information in
the pdb file.

a step earlier in tleap, i had to addAtomTypes YN and YC, however, there
was no way to specify them with "sp" hybridization, but "sp2" resulting
in two lines each containing a single bond between these two atoms
within the "!entry.C3N.unit.connectivity table" section of the ch3cn.lib
file (seems to be a double bond).

is this issue negligible, since the force constants and equilibrium
angles (180 degrees) are already describing the right molecule?

vedat




Alan schrieb:
> Nice, glad you did progress. See below.
>
> On Thu, May 20, 2010 at 12:38,  > wrote:
>
> thanks for your helpful hints. i updated acpype, created a pdb
> file with
> a single molecule and ran
>
> acpype -i ch3cn_210_single.pdb
>
> which generated an .itp and other interesting files. that's
> nice. (remember, i want to use gromacs with amber99sb force field
> and i
> downloaded 3 files from the amber site: ch3cn_210.pdb,
> frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)
>
> 1) the charges do not match the ones listed in the prep.ch3cn file.
> shall i just change them by hand accordingly?
>
>
> It doesn't match because it's using am1bcc, which was parametrised to
> reproduce the RESP charges, but obviously (sqm is semi-empirical
> method, not like gaussian)  it won't be accurate.
>
> However, you're right, if you have the RESP charges in prep.ch3cn just
> copy them by hand accordingly.
>
> Or even better, if you want to learn more about the whole stuff,
> double check if the parameters you got from the Manchester site are
> OK, why not trying q4md-forcefieldtools.org/RED/
> ? Once you got the charges (they
> should be very close if not the same from  prep.ch3cn), you can use
> acpype just to generate the topology by providing a c3n.MOL2 file with
> the charges calculated by RED and then using "acpype -di c3n.mol2 -c
> user".
>  
>
> 2) dummy atoms as listed in the prep.ch3cn are not present in the new
> .itp file.
>
>
> I guess you don't know how a prep file works, so
> see http://ambermd.org/doc/prep.html.
>  
>
> 3) the force constants seem totally different. shall i again just
> adjust
> them to the original file obtained from the amber site?
>
>
> If using acpype with default mode, so you'd get GAFF parameters. You
> may want to try:
>
> acpype -di c3n.mol2 -c user -a amber
>
> However, it still may diff. If you read Jaime's paper and you agree
> with what he did, so you can "copy&paste" his parameters as well.
>  
>
> is there another way of using acpype, with a proper args list, that i
> should use in this situation?
>
>
> Read the Wikis in the acpype site and 'acpype -h'. I am always keen
> for suggestions.
>
> Another possible way, would be using tleap from AmberTools, generate
> just one molecule, save parameters and use acpype to convert from
> amber to gromacs, something like
>
> acpype -p c3n.prmtop -x c3n.inpcrd
>
> If doing so, you'd get the exactly Jaime's topology but in gromacs
> format (gro and top file, not itp, so you may need to adjust things in
> the top file in order to create a itp, but should be a simple task).
>
> > BTW, how did you get this message "cannot find template for residue
> > C3N in our library"?
> i got that message *within* the following output when running:
> >acpype -i ch3cn_210.pdb
> [...]
> Warning: cannot find template for residue C3N

[gmx-users] Re: acetonitrile from amber to gromacs

[Alan]

Nice, glad you did progress. See below.

On Thu, May 20, 2010 at 12:38,  wrote:

> thanks for your helpful hints. i updated acpype, created a pdb file with
> a single molecule and ran
>
> acpype -i ch3cn_210_single.pdb
>
> which generated an .itp and other interesting files. that's
> nice. (remember, i want to use gromacs with amber99sb force field and i
> downloaded 3 files from the amber site: ch3cn_210.pdb,
> frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)
>
> 1) the charges do not match the ones listed in the prep.ch3cn file.
> shall i just change them by hand accordingly?
>

It doesn't match because it's using am1bcc, which was parametrised to
reproduce the RESP charges, but obviously (sqm is semi-empirical method, not
like gaussian)  it won't be accurate.

However, you're right, if you have the RESP charges in prep.ch3cn just copy
them by hand accordingly.

Or even better, if you want to learn more about the whole stuff, double
check if the parameters you got from the Manchester site are OK, why not
trying q4md-forcefieldtools.org/RED/? Once you got the charges (they should
be very close if not the same from  prep.ch3cn), you can use acpype just to
generate the topology by providing a c3n.MOL2 file with the charges
calculated by RED and then using "acpype -di c3n.mol2 -c user".


> 2) dummy atoms as listed in the prep.ch3cn are not present in the new
> .itp file.
>

I guess you don't know how a prep file works, so see
http://ambermd.org/doc/prep.html.


>  3) the force constants seem totally different. shall i again just adjust
> them to the original file obtained from the amber site?
>

If using acpype with default mode, so you'd get GAFF parameters. You may
want to try:

acpype -di c3n.mol2 -c user -a amber

However, it still may diff. If you read Jaime's paper and you agree with
what he did, so you can "copy&paste" his parameters as well.


>  is there another way of using acpype, with a proper args list, that i
> should use in this situation?
>

Read the Wikis in the acpype site and 'acpype -h'. I am always keen for
suggestions.

Another possible way, would be using tleap from AmberTools, generate just
one molecule, save parameters and use acpype to convert from amber to
gromacs, something like

acpype -p c3n.prmtop -x c3n.inpcrd

If doing so, you'd get the exactly Jaime's topology but in gromacs format
(gro and top file, not itp, so you may need to adjust things in the top file
in order to create a itp, but should be a simple task).

> BTW, how did you get this message "cannot find template for residue
> > C3N in our library"?
> i got that message *within* the following output when running:
> >acpype -i ch3cn_210.pdb
> [...]
> Warning: cannot find template for residue C3N in our library.
> You will not be able to save prmtop for this molecule.
> Warning: cannot find template for residue C3N in our library.
> You will not be able to save prmtop for this molecule.
> [gtkleap]$ #check C3N
> [gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd
> Error: dparm pchg does not exist!
>
>
> ++end_quote+
> ERROR: Sleap failed
> ==> Removing temporary files...
> ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd'
> Total time of execution: 7s
>

Ah, ok, I should've know this... It's a fall back routine to try to use
'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately.

Thanks for trying acpype.

Cheers,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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Re: [gmx-users] Re: acetonitrile from amber to gromacs

[vedat durmaz]

Alan schrieb:
> Dear Vedat,
>
> On Wed, May 19, 2010 at 20:36,  > wrote:
>
> @rui
> acpypi -i ch3cn_210.pdb
> says: "cannot find template for residue C3N in our library". and
> indeed,
> there's no residue C3N in my ffamber99sb.rtp file
>
> (and i don't know, how to use it in order to generate my topology
> or even
> an rtp file?!)
>
>
> Have a bit of patience and try to read a bit more about ACPYPE.
>
> 1) Read the info there, I am sure you'll find it useful;
> 2) You'll learn that you need to have just one molecule in a pdb and
> not the whole box if you want the topologi of C3N.
> 3) It took me 2s to get the topology with acpype but months to write
> the code, so if you'd take some few minutes to read and use an updated
> version (it's not acpypi anymore BTW)...
>
thanks for your helpful hints. i updated acpype, created a pdb file with
a single molecule and ran

acpype -i ch3cn_210_single.pdb

which generated an .itp and other interesting files. that's
nice. (remember, i want to use gromacs with amber99sb force field and i
downloaded 3 files from the amber site: ch3cn_210.pdb,
frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)

1) the charges do not match the ones listed in the prep.ch3cn file.
shall i just change them by hand accordingly?
2) dummy atoms as listed in the prep.ch3cn are not present in the new
.itp file.
3) the force constants seem totally different. shall i again just adjust
them to the original file obtained from the amber site?

is there another way of using acpype, with a proper args list, that i
should use in this situation?

i know, that's many questions, but is has to be done!

> BTW, how did you get this message "cannot find template for residue
> C3N in our library"?
i got that message *within* the following output when running:
>acpype -i ch3cn_210.pdb
[...]
Warning: cannot find template for residue C3N in our library.
 You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue C3N in our library.
 You will not be able to save prmtop for this molecule.
[gtkleap]$ #check C3N
[gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd
Error: dparm pchg does not exist!

++end_quote+
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd'
Total time of execution: 7s


>
> acpype.googlecode.com 
>
> Regards,
> Alan
>
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
-- 
gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Re: acetonitrile from amber to gromacs

[Alan]

Dear Vedat,

On Wed, May 19, 2010 at 20:36,  wrote:

> @rui
> acpypi -i ch3cn_210.pdb
> says: "cannot find template for residue C3N in our library". and indeed,
> there's no residue C3N in my ffamber99sb.rtp file
>
> (and i don't know, how to use it in order to generate my topology or even
> an rtp file?!)
>

Have a bit of patience and try to read a bit more about ACPYPE.

1) Read the info there, I am sure you'll find it useful;
2) You'll learn that you need to have just one molecule in a pdb and not the
whole box if you want the topologi of C3N.
3) It took me 2s to get the topology with acpype but months to write the
code, so if you'd take some few minutes to read and use an updated version
(it's not acpypi anymore BTW)...

BTW, how did you get this message "cannot find template for residue C3N in
our library"?

acpype.googlecode.com

Regards,
Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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!
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[gmx-users] Re: acetonitrile from amber to gromacs

[Vitaly Chaban]

>
> hi all together,
>
> this week i'm trying to do some simulations with acetonitrile (AN) as a
> solvent and using ffamber99 as force field. on this website
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
>
> i found a gorgeous little box containing a pretty number of 6-site
> modeled AN molecules, represented by 3 files:
>
> ch3cn_210.pdb
> frcmod.ch3cn
> prep.ch3cn
>
> does anyone have an idea, how to generate .gro/.itp files out of these
> amber files, preferably by pushing a single button of some proper tool??
>
> i'ld be the happiest guy in world if someone told me the trick!
>
>
To traslate PDB into GRO, use editconf (gromacs utility).
To get ITP, use X2TOP (gromacs utility).

Also see the topology archive on the gromacs website. A few years ago I
uploaded some working examples with ACN.


-- 
Dr. Vitaly Chaban
-- 
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