[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Berk Hess
gmx3 at hotmail.com
Wed Aug 25 14:34:30 CEST 2010
Hi,
I fixed all the terminal residue issues.
The automatic HIE terminal translation is still swtiched by the env.var.
I'm still thinking if there could be issues when we turn that always on.
Berk
From: alanwilter at gmail.com
Date: Tue, 24 Aug 2010 22:55:57 +0100
Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
To: gmx-users at gromacs.org
Dear Berk,
I understand your point and this can be very confusing.
I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but this is not working either with rev. d6298. Error:
[snip]Which HISTIDINE type do you want for residue 30. H on ND1 only (HID)1. H on NE2 only (HIE)2. H on ND1 and NE2 (HIP)3. Coupled to Heme (HIS1)
Type a number:1Identified residue HIS1 as a starting terminus.Identified residue HIS3 as a ending terminus.8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix: HIS1 HIS2 NE214 NE231 HIS2 NE231 0.854 HIS3 NE248 0.751 0.847
-------------------------------------------------------Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line: 552
Fatal error:Residue 'HISE' not found in residue topology databaseFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
The pdb I am using is hhh.pdb ATOM 1 N HIS 1 3.389 1.609 -0.001 1.00 0.00 NATOM 2 H1 HIS 1 4.107 0.893 -0.048 1.00 0.00 H
ATOM 3 H2 HIS 1 2.795 1.549 -0.816 1.00 0.00 HATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00 HATOM 5 CA HIS 1 4.058 2.928 0.075 1.00 0.00 C
ATOM 6 HA HIS 1 3.894 3.469 -0.857 1.00 0.00 HATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00 CATOM 8 HB2 HIS 1 2.384 3.783 1.126 1.00 0.00 H
ATOM 9 HB3 HIS 1 3.695 3.231 2.164 1.00 0.00 HATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00 CATOM 11 ND1 HIS 1 4.013 5.834 2.591 1.00 0.00 N
ATOM 12 CE1 HIS 1 4.604 7.011 2.356 1.00 0.00 CATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00 HATOM 14 NE2 HIS 1 4.919 7.122 1.056 1.00 0.00 N
ATOM 15 HE2 HIS 1 5.505 7.845 0.657 1.00 0.00 HATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00 CATOM 17 HD2 HIS 1 4.620 5.781 -0.645 1.00 0.00 H
ATOM 18 C HIS 1 5.564 2.693 0.196 1.00 0.00 CATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00 OATOM 20 N HIS 2 6.376 3.718 -0.053 1.00 0.00 N
ATOM 21 H HIS 2 5.980 4.646 -0.135 1.00 0.00 HATOM 22 CA HIS 2 7.843 3.744 -0.109 1.00 0.00 CATOM 23 HA HIS 2 8.260 3.319 0.806 1.00 0.00 H
ATOM 24 CB HIS 2 8.319 2.925 -1.327 1.00 0.00 CATOM 25 HB2 HIS 2 7.855 1.940 -1.312 1.00 0.00 HATOM 26 HB3 HIS 2 7.985 3.435 -2.233 1.00 0.00 H
ATOM 27 CG HIS 2 9.807 2.703 -1.450 1.00 0.00 CATOM 28 ND1 HIS 2 10.461 2.463 -2.655 1.00 0.00 NATOM 29 CE1 HIS 2 11.770 2.542 -2.382 1.00 0.00 C
ATOM 30 HE1 HIS 2 12.557 2.484 -3.124 1.00 0.00 HATOM 31 NE2 HIS 2 11.969 2.794 -1.078 1.00 0.00 NATOM 32 HE2 HIS 2 12.817 3.173 -0.672 1.00 0.00 H
ATOM 33 CD2 HIS 2 10.740 2.839 -0.459 1.00 0.00 CATOM 34 HD2 HIS 2 10.579 3.098 0.574 1.00 0.00 HATOM 35 C HIS 2 8.279 5.228 -0.214 1.00 0.00 C
ATOM 36 O HIS 2 7.440 6.079 -0.525 1.00 0.00 OATOM 37 N HIS 3 9.547 5.520 0.075 1.00 0.00 NATOM 38 H HIS 3 10.192 4.759 0.245 1.00 0.00 H
ATOM 39 CA HIS 3 10.254 6.807 0.049 1.00 0.00 CATOM 40 HA HIS 3 10.021 7.358 -0.860 1.00 0.00 HATOM 41 CB HIS 3 9.841 7.621 1.297 1.00 0.00 C
ATOM 42 HB2 HIS 3 8.754 7.687 1.320 1.00 0.00 HATOM 43 HB3 HIS 3 10.158 7.074 2.185 1.00 0.00 HATOM 44 CG HIS 3 10.359 9.037 1.429 1.00 0.00 C
ATOM 45 ND1 HIS 3 10.137 9.848 2.546 1.00 0.00 NATOM 46 CE1 HIS 3 10.788 10.994 2.308 1.00 0.00 CATOM 47 HE1 HIS 3 10.849 11.818 3.006 1.00 0.00 H
ATOM 48 NE2 HIS 3 11.375 10.962 1.100 1.00 0.00 NATOM 49 HE2 HIS 3 11.977 11.674 0.715 1.00 0.00 HATOM 50 CD2 HIS 3 11.100 9.742 0.525 1.00 0.00 C
ATOM 51 HD2 HIS 3 11.456 9.376 -0.428 1.00 0.00 HATOM 52 C HIS 3 11.761 6.487 0.002 1.00 0.00 CATOM 53 O HIS 3 12.128 5.407 0.518 1.00 0.00 O
ATOM 54 OXT HIS 3 12.494 7.275 -0.632 1.00 0.00 O
Now, using HIE (HHH.pdb, like hhh.pdb but HIE for res instead of HIS) with export GMX_FFRTP_TER_RENAME=1 and then
pdb2gmx -f HHH.pdb -o HHH.pdb -p agHHH.top -ff amber99sb -water none
works.
echo 1 1 1 | pdb2gmx -f hhh.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none -his
will work as well as long as I replace HB3 by HB1 or use -ignh, but attention, without GMX_FFRTP_TER_RENAME, it doesn't work.
I hope it can help.
Cheers,
Alan
On 24 August 2010 20:14, Berk Hess <gmx3 at hotmail.com> wrote:
Hi,
I asked the authors of the gmx amber ports what the desired behavior would be.
For the time being I committed the fix, but it only gets activated when you have
the env.var. GMX_FFRTP_TER_RENAME set.
Berk
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Date: Tue, 24 Aug 2010 20:48:05 +0200
Hi,
I have made a fix, but am now wondering if we actually want to fix this.
HIE is not a standard pdb residue name.
A file with HIS-HIS-HIS would work.
HIE is an Amber name and in that case one might say that you should use:
NHIE-HIE-CHIE.
But I don't know what the Amber program would support for input.
PS NHIE is now listed incorrectly as NHISE in residuetypes.dat,
so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that.
Berk
From: alanwilter at gmail.com
Date: Tue, 24 Aug 2010 18:06:45 +0100
Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
To: gmx-users at gromacs.org
I am using gmx 4.5 d748b.
Thanks Berk, it seems to be working ... for DNA.
But this one is broken (and it was working before): HHH is tripetide Hie-Hie-Hie.
pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none
[snip]Identified residue HIE1 as a starting terminus.Identified residue HIE3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748bSource code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916
Fatal error:There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Alan
On 24 August 2010 15:30, Berk Hess <gmx3 at hotmail.com> wrote:
Hi,
I fixed it.
Thanks for the fast test and the complete instructions,
Berk
From: alanwilter at gmail.com
Date: Tue, 24 Aug 2010 15:22:34 +0100
To: gmx-users at gromacs.org
Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Hi there, in special Berk.
So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing:
wget -c "http://www.pdbe.org/download/1BNA" -O 1BNA.pdb
grep 'ATOM ' 1BNA.pdb >| DNA.pdb
cat << EOF >| SPE.mdpdefine = -DFLEXIBLEintegrator = mdnsteps = 0
dt = 0.001constraints = noneemtol = 10.0emstep = 0.01nstcomm = 1ns_type = simple
nstlist = 0rlist = 0rcoulomb = 0rvdw = 0Tcoupl = noPcoupl = no
gen_vel = nonstxout = 1pbc = nonstlog = 1nstenergy = 1nstvout = 1nstfout = 1nstxtcout = 1
comm_mode = ANGULARcontinuation = yesEOF
pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45[snip]
8 out of 8 lines of specbond.dat converted successfully[1] 42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p
with 5e347 it worded fine, i.e, it opens files
Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arnOpening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
and proceed.
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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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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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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