[gmx-users] Amber to Gromacs
Nash, Anthony
Anthony.Nash at warwick.ac.uk
Wed Apr 30 18:17:30 CEST 2014
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 ]
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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