[gmx-users] Amber to Gromacs

Justin Lemkul jalemkul at vt.edu
Wed Apr 30 18:52:09 CEST 2014 


On 4/30/14, 12:17 PM, Nash, Anthony wrote:
> 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:
>

If PHE is the first residue in the chain, PHE is not your problem.  pdb2gmx 
tells you that whatever residue 11 in the chain is the problem.  It would also 
help if you upgraded to a non-archaic version of Gromacs; the error messages 
have become vastly more descriptive.

-Justin

> [ PHE ]
>   [ atoms ]
>       N    N           -0.41570     1
>       H    H            0.27190     2
>      CA    CT          -0.00240     3
>      HA    H1           0.09780     4
>      CB    CT          -0.03430     5
>     HB1    HC           0.02950     6
>     HB2    HC           0.02950     7
>      CG    CA           0.01180     8
>     CD1    CA          -0.12560     9
>     HD1    HA           0.13300    10
>     CE1    CA          -0.17040    11
>     HE1    HA           0.14300    12
>      CZ    CA          -0.10720    13
>      HZ    HA           0.12970    14
>     CE2    CA          -0.17040    15
>     HE2    HA           0.14300    16
>     CD2    CA          -0.12560    17
>     HD2    HA           0.13300    18
>       C    C            0.59730    19
>       O    O           -0.56790    20
>
>
> 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-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Nash, Anthony [Anthony.Nash at warwick.ac.uk]
> Sent: 30 April 2014 14:09
> To: gmx-users at 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-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: 30 April 2014 13:29
> To: gmx-users at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
==================================================

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

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

==================================================

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