[gmx-users] ATB and PRODRG

[‪farial tavakoli‬ ‪]

Dear gmx users
I am using gromos96 54 a7 and gromos 96 a1 force fiels to simulate tow various 
complexes  ( protein + ligand). and  used ATB and PRODRG  to create topology 
files for them, respectively. I dont know anything about editing ATB and 
PRODRG' topology files but reassigingn their charges and charge groups . Is 
there anything else that I have to do to create a proper  topology file for 
GROMOACS?I would really appreciate for any help. 
Thanks in advanceFarial 
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Re: [gmx-users] ATB topology: itp to top conversion

[Anna Lappala]

Thank you Mark and Justin! That makes sense, of course!!! Many thanks.

With best wishes 
Anna

> On Jun 13, 2017, at 17:22, Mark Abraham  wrote:
> 
> Hi,
> 
>> On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala  wrote:
>> 
>> Dear all,
>> 
>> I am confused: I have my pdb file as well as the itp file produced by ATB.
>> I want to convert these into top and gro files but the molecule is not
>> recognised by the forcefield when I do the following:
>> 
>> pdb2gmx -f input.pdb -o output.gro -i topology.itp
>> 
> 
> pdb2gmx is mostly for matching stuff found in .rtp files to produce .itp
> files. You already have your .itp file.
> 
> 
>> I have looked through tutorials and on the mailing list, but mostly the
>> workaround is to #include the itp file into an existing top file - which i
>> do not have because i only have a heteromolecule, and no protein...
>> 
> 
> The .top files are intended to be edited and written, e.g.
> 
> #include "your.ff/forcefield.itp"
> #include "heteromolecule.itp"
> #include "your.ff/spc.itp"
> [system]
> whatever name you like
> [molecules]
> hetero 1
> SOL 10123
> 
> Mark
> 
> 
>> Many thanks for any suggestions.
>> Anna
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Re: [gmx-users] ATB topology: itp to top conversion

[Mark Abraham]

Hi,

On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala  wrote:

> Dear all,
>
> I am confused: I have my pdb file as well as the itp file produced by ATB.
> I want to convert these into top and gro files but the molecule is not
> recognised by the forcefield when I do the following:
>
> pdb2gmx -f input.pdb -o output.gro -i topology.itp
>

pdb2gmx is mostly for matching stuff found in .rtp files to produce .itp
files. You already have your .itp file.


> I have looked through tutorials and on the mailing list, but mostly the
> workaround is to #include the itp file into an existing top file - which i
> do not have because i only have a heteromolecule, and no protein...
>

The .top files are intended to be edited and written, e.g.

#include "your.ff/forcefield.itp"
#include "heteromolecule.itp"
#include "your.ff/spc.itp"
[system]
whatever name you like
[molecules]
hetero 1
SOL 10123

Mark


> Many thanks for any suggestions.
> Anna
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>
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Re: [gmx-users] ATB topology: itp to top conversion

[Justin Lemkul]

On 6/13/17 7:06 PM, Anna Lappala wrote:

Dear all,

I am confused: I have my pdb file as well as the itp file produced by ATB. I 
want to convert these into top and gro files but the molecule is not recognised 
by the forcefield when I do the following:

pdb2gmx -f input.pdb -o output.gro -i topology.itp

I have looked through tutorials and on the mailing list, but mostly the 
workaround is to #include the itp file into an existing top file - which i do 
not have because i only have a heteromolecule, and no protein...



The purpose of pdb2gmx is to write a topology.  You already have that.  The .itp 
format (typically the topology of a single entity) is hardly different from that 
of a .top (which is a system topology).  A .top file:


1. #includes or otherwise has parameters from a parent force field
2. Has a [system] directive
3. Has a [molecules] directive

Your topology from ATB is based on a GROMOS force field parameter set, which is 
probably already in GROMACS and you can therefore start your .top with a 
suitable #include statement to that parent force field.  Then #include your 
.itp, add [system] and [molecules], and you have a functional .top file.


As for format conversion, use editconf, not pdb2gmx.  But you don't have to use 
.gro (a common misconception).


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] ATB topology: itp to top conversion

[Anna Lappala]

Dear all,

I am confused: I have my pdb file as well as the itp file produced by ATB. I 
want to convert these into top and gro files but the molecule is not recognised 
by the forcefield when I do the following:

pdb2gmx -f input.pdb -o output.gro -i topology.itp 

I have looked through tutorials and on the mailing list, but mostly the 
workaround is to #include the itp file into an existing top file - which i do 
not have because i only have a heteromolecule, and no protein...

Many thanks for any suggestions.
Anna
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[gmx-users] ATB parametrization of small molecule

[Sun Iba]

Hello everyone

I want to simulate a protein ligand docked complex using GROMOS96 43a1
force field. I have prepared the ligand topology using ATB server. However,
I want to know how can I validate the results of ATB when no experimental
or computational data is available for small molecule.
I have read in Justin's paper that we can calculate octanol-water partition
coefficient in biphasic system and correlate the logP and other paramteres
with available data. However, in the absence of any experimental or
theoretical proof, is there any way by which I can validate the ATB
parameters? The small molecule contains groups fllowing groups:
N=N, OCH3, Phenyl rings, Cyclohexyl group, -CN, Vinyl group.

Thank you
Suniba
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Re: [gmx-users] ATB server (charge assign)

[Justin Lemkul]

On 7/11/16 2:14 AM, elham tazikeh wrote:

Dear Justin
thanks for your good advise
as you're mentioned, i must include necessary file next to other force
field files in my directory
my version of gromaces is 4.6.5, and my force field is gromos 53a6

1-concerning below message, which ones is appropriate for me?
Gromacs3.x.x-4.0.x 53a6-54a7
or
Gromacs 4.5.x-5.x.x53a6



I don't know why you would need either of these from ATB; the GROMOS force 
fields are already provided in GROMACS.



2-also, United-Atom PDB (original geometry)

will
be (*.pdb ) and needs to editconf to convert ( *.gro)...coordinate file
and
GROMACS G53A6FF United-Atom (ITP file)

will
be (*.itp)topology file

Is it right?



It is a common misconception that one *needs* a .gro file; a .pdb works just 
fine, but certainly you can convert it if you want.


Your links don't work because they are not publicly accessible.  But ATB should 
be very straightforward in terms of presenting you with what you need.



3-coud you please tell me, when i should get those files (*.pdb and *.itp)?
before include proposed new files in my directory or after that?



I don't understand this.  Perhaps it will be useful to follow along with a 
tutorial: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html


-Justin


Regards
elham

Warning! This molecule contains non-standard atom types not included in the
standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the
internal GROMACS parameter files must be updated. These can be downloaded
using the link below. Instructions on where to place (and how to use) the
files are provided in the README file included in the archive.

Gromacs 3.x.x-4.0.x 53a6 - 54a7
 Gromacs
4.5.x-5.x.x 53a6




--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] ATB server (charge assign)

[elham tazikeh]

Dear Justin
thanks for your good advise
as you're mentioned, i must include necessary file next to other force
field files in my directory
my version of gromaces is 4.6.5, and my force field is gromos 53a6

1-concerning below message, which ones is appropriate for me?
Gromacs3.x.x-4.0.x 53a6-54a7
or
Gromacs 4.5.x-5.x.x53a6

2-also, United-Atom PDB (original geometry)

will
be (*.pdb ) and needs to editconf to convert ( *.gro)...coordinate file
and
GROMACS G53A6FF United-Atom (ITP file)

will
be (*.itp)topology file

Is it right?

3-coud you please tell me, when i should get those files (*.pdb and *.itp)?
before include proposed new files in my directory or after that?

Regards
elham

Warning! This molecule contains non-standard atom types not included in the
standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the
internal GROMACS parameter files must be updated. These can be downloaded
using the link below. Instructions on where to place (and how to use) the
files are provided in the README file included in the archive.

Gromacs 3.x.x-4.0.x 53a6 - 54a7
 Gromacs
4.5.x-5.x.x 53a6

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[gmx-users] ATB

[Vasiliy Znamenskiy]

Dear All

Does the type of chemical bond (single, double, triple), built by JSME
Molecular Editor, directly influence on the final results of Automated
Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of
built protons?
I built a molecule with a some double bond, number of protons is correct,
however finally ATB's Show structure option shows this bond as a single
bond, however number of protons there as for a double bond.
Is it an error of visualization only or built topology files have errors?

Thank you,
Vasiliy
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Re: [gmx-users] ATB

[Justin Lemkul]

On 4/1/15 8:30 AM, Vasiliy Znamenskiy wrote:

Dear All

Does the type of chemical bond (single, double, triple), built by JSME
Molecular Editor, directly influence on the final results of Automated
Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of
built protons?
I built a molecule with a some double bond, number of protons is correct,
however finally ATB's Show structure option shows this bond as a single
bond, however number of protons there as for a double bond.
Is it an error of visualization only or built topology files have errors?



The topology is definitive, not whatever is rendered.  That goes for all 
software.  Most aren't intelligent enough to represent bond order correctly.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] ATB SERVER

[Mahboobeh Eslami]

hi my friends
I use ATB server for my ligands.
which are itp and pdb file used for ligands in md simulation by gromacs.
thanks a lot
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Re: [gmx-users] ATB SERVER

[Mark Abraham]

There are probably a few tutorials that describe what you're trying to do.
Probably none of them are  exactly right, but you will learn from doing
them regardless.

Please do a preliminary search for information before asking questions! :-)

Mark
On Dec 1, 2013 10:38 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com
wrote:

 hi my friends
 I use ATB server for my ligands.
 which are itp and pdb file used for ligands in md simulation by gromacs.
 thanks a lot
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