[gmx-users] Amber to GROMACS structure/topology

[Gustavo Avelar Molina]

Hi,

I would like to know if there is a way to convert Amber structures and
topologies to the GROMACS format.

Thank you very much for your time.

Best regards,

Gustavo

==
Gustavo Avelar Molina, B.Sc. Chem.
M.Sc. Chem. Student

Department of Chemistry
Faculty of Philosophy, Sciences and Literature of Ribeirão Preto
Protein Biochemistry and Biophysics Laboratory
University of São Paulo, Ribeirão Preto, São Paulo, Brazil

+55 16 994311221 | +55 11 949874141

avelarmolinagust...@gmail.com | gustavoavelarmol...@usp.br

https://lbbpusp.wordpress.com/ |





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Re: [gmx-users] Amber to GROMACS structure/topology

[Michael Shirts]

http://parmed.github.io/ParmEd/html/index.html

https://code.google.com/p/acpype/

On Thu, Sep 24, 2015 at 5:14 PM, Gustavo Avelar Molina
 wrote:
> Hi,
>
> I would like to know if there is a way to convert Amber structures and
> topologies to the GROMACS format.
>
> Thank you very much for your time.
>
> Best regards,
>
> Gustavo
>
> ==
> Gustavo Avelar Molina, B.Sc. Chem.
> M.Sc. Chem. Student
>
> Department of Chemistry
> Faculty of Philosophy, Sciences and Literature of Ribeirão Preto
> Protein Biochemistry and Biophysics Laboratory
> University of São Paulo, Ribeirão Preto, São Paulo, Brazil
>
> +55 16 994311221 | +55 11 949874141
>
> avelarmolinagust...@gmail.com | gustavoavelarmol...@usp.br
>
> https://lbbpusp.wordpress.com/ |
>
> 
> 
> 
>
> ==
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[gmx-users] amber to gromacs conversion of LJ potential

[Chetan Mahajan]

Dear All,

While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:

sigma = 2 * r * 2^(-1/6)

I understand the factor 2^(-1/6), but there is another 2 that appears in
the beginning. Where is that factor coming from? That factor does not arise
when we choose following forms for LJ potential functions in Amber as well
as Gromacs.

Amber:

[image: Inline image 1]

Gromacs:

[image: Inline image 2]

Thanks in advance!

regards
Chetan
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[gmx-users] Amber to Gromacs

[Nash, Anthony]

Hi All,

I've been thrown upon a project which requires the use of the Amber FF. I have 
a crystal structure .pdb and I wish to make a topology file using the AMBER 
ff99SB forcefield. The gromacs website directs me to the ffamber ports program, 
which seems to require Gromacs versions 3.1.4, 3.2.1, . 4.0. I, however, 
have access to Gromacs 4.6.1. Must I install an old version of Gromacs? If I 
must, what kind of issues am I going to face when I take my 3.* generated 
Gromacs topology file and run it on version 4.6.1? Or is this very out of date 
and there is something new?

Thanks for any help. Apologies if these seem quite basic or I am a bit behind 
with the times, I've been doing DFT calculations for the last year and I am 
trying to get my Gromacs hat back on!

Thanks
Anthony 
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Re: [gmx-users] Amber to Gromacs

[Justin Lemkul]

On 4/30/14, 8:25 AM, Nash, Anthony wrote:

Hi All,

I've been thrown upon a project which requires the use of the Amber FF. I have 
a crystal structure .pdb and I wish to make a topology file using the AMBER 
ff99SB forcefield. The gromacs website directs me to the ffamber ports program, 
which seems to require Gromacs versions 3.1.4, 3.2.1, . 4.0. I, however, 
have access to Gromacs 4.6.1. Must I install an old version of Gromacs? If I 
must, what kind of issues am I going to face when I take my 3.* generated 
Gromacs topology file and run it on version 4.6.1? Or is this very out of date 
and there is something new?



Most of the Amber force fields are supported natively now; there is no need to 
download the ffamber ports so that information is indeed outdated.  Amber99-SB 
and Amber99-SB-ILDN are both built into Gromacs.


-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] Amber to Gromacs

[Nash, Anthony]

Wow! I am out of date. 

As always, thanks for the help Justin.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: 30 April 2014 13:29
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Amber to Gromacs

On 4/30/14, 8:25 AM, Nash, Anthony wrote:
 Hi All,

 I've been thrown upon a project which requires the use of the Amber FF. I 
 have a crystal structure .pdb and I wish to make a topology file using the 
 AMBER ff99SB forcefield. The gromacs website directs me to the ffamber ports 
 program, which seems to require Gromacs versions 3.1.4, 3.2.1, . 4.0. I, 
 however, have access to Gromacs 4.6.1. Must I install an old version of 
 Gromacs? If I must, what kind of issues am I going to face when I take my 3.* 
 generated Gromacs topology file and run it on version 4.6.1? Or is this very 
 out of date and there is something new?


Most of the Amber force fields are supported natively now; there is no need to
download the ffamber ports so that information is indeed outdated.  Amber99-SB
and Amber99-SB-ILDN are both built into Gromacs.

-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] Amber to Gromacs

[Nash, Anthony]

Hi Justin,

I wonder if you could advice, I am a little further ahead than I was before. I 
am using an crystal structure .pdb from the protein data bank. There are no 
hydrogen atoms. I assume, given the pdb2gmx that this is taken care of unless 
the -ignh is selected.

I am getting a painful error upon running pdb2gmx_d -f 4AUO_mono.pdb -water 
tip3p

Opening force field file 
/Users/Anthony/gromacs451/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file 
/Users/Anthony/gromacs451/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file 
/Users/Anthony/gromacs451/share/gromacs/top/amber99sb.ff/rna.arn
Checking for duplicate atoms


Processing chain 1 'A' (2986 atoms, 367 residues)
There are 568 donors and 543 acceptors
There are 786 hydrogen bonds
Will use HISE for residue 94
Will use HISE for residue 113
Will use HISE for residue 149
Will use HISE for residue 164
Will use HISE for residue 177
Will use HISE for residue 194
Will use HISE for residue 199
Will use HISE for residue 203
Will use HISE for residue 209
Will use HISE for residue 339
Will use HISE for residue 357
Will use HISE for residue 398
Will use HISE for residue 405
Will use HISE for residue 421
Identified residue PHE81 as a starting terminus.
Identified residue CYS447 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   HIS94  HIS113  MET141  HIS149  HIS164  HIS177  HIS194
  NE2117  NE2275   SD493  NE2559  NE2668  NE2754  NE2916
..
...
..  [DISTANCE MATRIX HERE]
..
..
Linking CYS-259 SG-1396 and CYS-447 SG-2985...
Opening force field file 
/Users/Anthony/gromacs451/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file 
/Users/Anthony/gromacs451/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file 
/Users/Anthony/gromacs451/share/gromacs/top/amber99sb.ff/rna.arn
Checking for duplicate atoms

---
Program pdb2gmx_d, VERSION 4.5.1
Source code file: pgutil.c, line: 88

Fatal error:
Atom CG not found in residue seq.nr. 11 while adding atom
---


The first residue entry is:
ATOM  1  N   PHE A  81  17.085 132.505  30.006  1.00 16.87   N
ATOM  2  CA  PHE A  81  16.981 132.301  28.532  1.00 16.72   C
ATOM  3  C   PHE A  81  18.222 132.817  27.799  1.00 16.36   C
ATOM  4  O   PHE A  81  18.921 133.701  28.291  1.00 17.46   O
ATOM  5  CB  PHE A  81  15.724 133.005  27.999  1.00 15.39   C
ATOM  6  CG  PHE A  81  15.813 134.516  27.977  1.00 11.26   C
ATOM  7  CD1 PHE A  81  16.603 135.176  27.035  1.00  8.12   C
ATOM  8  CD2 PHE A  81  15.060 135.275  28.858  1.00 10.00   C
ATOM  9  CE1 PHE A  81  16.640 136.574  26.968  1.00  6.93   C
ATOM 10  CE2 PHE A  81  15.092 136.678  28.794  1.00 10.62   C
ATOM 11  CZ  PHE A  81  15.885 137.326  27.844  1.00  7.00   C



Yet the Amberff99sb aminoacid.rtp file describes PHE as:

[ PHE ]
 [ atoms ]
 NN   -0.41570 1
 HH0.27190 2
CACT  -0.00240 3
HAH1   0.09780 4
CBCT  -0.03430 5
   HB1HC   0.02950 6
   HB2HC   0.02950 7
CGCA   0.01180 8
   CD1CA  -0.12560 9
   HD1HA   0.1330010
   CE1CA  -0.1704011
   HE1HA   0.1430012
CZCA  -0.1072013
HZHA   0.1297014
   CE2CA  -0.1704015
   HE2HA   0.1430016
   CD2CA  -0.1256017
   HD2HA   0.1330018
 CC0.5973019
 OO   -0.5679020


I am guessing that there is a bunch of atom mismatches. I am not really sure 
where to go from here. 

Many thanks
Anthony 










From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Nash, Anthony 
[anthony.n...@warwick.ac.uk]
Sent: 30 April 2014 14:09
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Amber to Gromacs

Wow! I am out of date.

As always, thanks for the help Justin.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: 30 April 2014 13:29
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Amber to Gromacs

On 4/30/14, 8:25 AM, Nash, Anthony wrote:
 Hi All,

 I've been thrown upon a project which requires the use of the Amber FF. I 
 have a crystal structure .pdb and I wish to make a topology file using the 
 AMBER ff99SB forcefield. The gromacs website directs me to the ffamber ports 
 program

[gmx-users] amber ff gromacs

[virk]

Dear People,

I am trying to simulate glycine molecule using amber ff. I have changed the
residues in pdb file with N and C respectively.
ATOM  1  NNGLY1  -1.476   0.232   0.252  1.00  0.00
ATOM  2  CA  CGLY1  -0.012   0.296   0.348  1.00  0.00
ATOM  3  CCGLY1   0.596  -0.652  -0.648  1.00  0.00
ATOM  4  O GLY 1  -0.124  -1.320  -1.368  1.00  0.00
ATOM  5  OXT GLY 1   1.916  -0.760  -0.740  1.00  0.00
ATOM  6  H3   GLY 1  -1.736  -0.252  -0.592  1.00  0.00
ATOM  7  HA2 GLY 1   0.292   0.020   1.364  1.00  0.00
ATOM  8  HA1 GLY 1   0.320   1.320   0.132  1.00  0.00
ATOM  9  HGLY 1  -1.636  -0.236   1.132  1.00  0.00
ATOM 10  H   GLY 1  -1.916   1.136   0.272  1.00  0.00
TER  11 GLY 1 
END 

But when I am using pdb2gmx, I am getting this error 
Residue 1 named NGLY of a molecule in the input file was mapped to an entry
in the topology database, but the atom CA used in that entry is not found in
the input file.

But atom CA is in the input pdb file and with same name in amber .rtp file
too. If I remove N and C prefixes in pdb file, pdb works for all other
fields.

I will be thankful for your help and time.

Kind Regards,
Amninder Virk
 

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[gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

Hello Everyone,

ambconv.tgz (
http://www.gromacs.org/Downloads/User_contributions/Other_software)  tool
exists for converting Amer input files into the ones for Gromacs. Now, it's
README-eng file says that two Amber input files ( .atop (topology)  and
.rst (coordinates) ) are needed to generate input files for Gromacs.
Corresponding file formats in current Amber version are .prmtop and .inpcrd
respectively. Are these formats, just like older ones, exactly compatible
with this tool? If not, are there other tools to convert Amber input files
into the ones for Gromacs?

If this tool can be used, is the condition of removing all water before
applying this tool mandatory?

Thank you.

regards
Chetan
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Re: [gmx-users] Amber to Gromacs conversion

[Barnett, James W.]

On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
 are there other tools to convert Amber input files
 into the ones for Gromacs?

I've had success with acpype:
https://code.google.com/p/acpype/

Use the amb2gmx mode:

acpype -p _prmtop_ -x _inpcrd_

-- 
Wes Barnett | jbarn...@tulane.edu
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

THis looks interesting, However, any version is giving following error on
test mentioned in README:

../acpype.py -i FFF.pdb
  File ../acpype.py, line 1231
with open(pklFile, wb) as f:  # for python 2.6 or higher
^
SyntaxError: invalid syntax

Unfortunately, I do not know python.

Thanks
Chetan


On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.eduwrote:

 On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
  are there other tools to convert Amber input files
  into the ones for Gromacs?

 I've had success with acpype:
 https://code.google.com/p/acpype/

 Use the amb2gmx mode:

 acpype -p _prmtop_ -x _inpcrd_

 --
 Wes Barnett | jbarn...@tulane.edu
 --
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

THis looks interesting, However, any version is giving following error on
test mentioned in README:

../acpype.py -i FFF.pdb
  File ../acpype.py, line 1231
with open(pklFile, wb) as f:  # for python 2.6 or higher
^
SyntaxError: invalid syntax

Unfortunately, I do not know python.

Thanks


On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.eduwrote:

 On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
  are there other tools to convert Amber input files
  into the ones for Gromacs?

 I've had success with acpype:
 https://code.google.com/p/acpype/

 Use the amb2gmx mode:

 acpype -p _prmtop_ -x _inpcrd_

 --
 Wes Barnett | jbarn...@tulane.edu
 --
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 posting!

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Re: [gmx-users] Amber to Gromacs conversion

[Barnett, James W.]

You shouldn't change any of the code unless you know what you're doing. If you 
remove lines it will not work as intended. 

I think you simply need to upgrade your version of Python 2, according to the 
error message.

jbarn...@tulane.edu | from mobile

Chetan Mahajan chetanv...@gmail.com wrote:

I did play around lines 1231 and 1232, by keeping 1232, while removing
1231, etc etc. No success so far!


On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan chetanv...@gmail.com wrote:

 THis looks interesting, However, any version is giving following error on
 test mentioned in README:

 ../acpype.py -i FFF.pdb
   File ../acpype.py, line 1231
 with open(pklFile, wb) as f:  # for python 2.6 or higher
 ^
 SyntaxError: invalid syntax

 Unfortunately, I do not know python.

 Thanks


 On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. 
 jbarn...@tulane.eduwrote:

 On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
  are there other tools to convert Amber input files
  into the ones for Gromacs?

 I've had success with acpype:
 https://code.google.com/p/acpype/

 Use the amb2gmx mode:

 acpype -p _prmtop_ -x _inpcrd_

 --
 Wes Barnett | jbarn...@tulane.edu
 --
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 posting!

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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

Thanks, James. I already have python 2.4.
regards
Chetan


On Tue, Dec 3, 2013 at 8:45 PM, Barnett, James W. jbarn...@tulane.eduwrote:

 You shouldn't change any of the code unless you know what you're doing. If
 you remove lines it will not work as intended.

 I think you simply need to upgrade your version of Python 2, according to
 the error message.

 jbarn...@tulane.edu | from mobile

 Chetan Mahajan chetanv...@gmail.com wrote:

 I did play around lines 1231 and 1232, by keeping 1232, while removing
 1231, etc etc. No success so far!
 
 
 On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan chetanv...@gmail.com
 wrote:
 
  THis looks interesting, However, any version is giving following error
 on
  test mentioned in README:
 
  ../acpype.py -i FFF.pdb
File ../acpype.py, line 1231
  with open(pklFile, wb) as f:  # for python 2.6 or higher
  ^
  SyntaxError: invalid syntax
 
  Unfortunately, I do not know python.
 
  Thanks
 
 
  On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.edu
 wrote:
 
  On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
   are there other tools to convert Amber input files
   into the ones for Gromacs?
 
  I've had success with acpype:
  https://code.google.com/p/acpype/
 
  Use the amb2gmx mode:
 
  acpype -p _prmtop_ -x _inpcrd_
 
  --
  Wes Barnett | jbarn...@tulane.edu
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