[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Alan
alanwilter at gmail.com
Tue Aug 24 23:55:57 CEST 2010
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 3
0. 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:1
Identified 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-d6298
Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line:
552
Fatal error:
Residue 'HISE' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website 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
N
ATOM 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
H
ATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00
H
ATOM 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
H
ATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00
C
ATOM 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
H
ATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00
C
ATOM 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
C
ATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00
H
ATOM 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
H
ATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00
C
ATOM 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
C
ATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00
O
ATOM 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
H
ATOM 22 CA HIS 2 7.843 3.744 -0.109 1.00 0.00
C
ATOM 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
C
ATOM 25 HB2 HIS 2 7.855 1.940 -1.312 1.00 0.00
H
ATOM 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
C
ATOM 28 ND1 HIS 2 10.461 2.463 -2.655 1.00 0.00
N
ATOM 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
H
ATOM 31 NE2 HIS 2 11.969 2.794 -1.078 1.00 0.00
N
ATOM 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
C
ATOM 34 HD2 HIS 2 10.579 3.098 0.574 1.00 0.00
H
ATOM 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
O
ATOM 37 N HIS 3 9.547 5.520 0.075 1.00 0.00
N
ATOM 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
C
ATOM 40 HA HIS 3 10.021 7.358 -0.860 1.00 0.00
H
ATOM 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
H
ATOM 43 HB3 HIS 3 10.158 7.074 2.185 1.00 0.00
H
ATOM 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
N
ATOM 46 CE1 HIS 3 10.788 10.994 2.308 1.00 0.00
C
ATOM 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
N
ATOM 49 HE2 HIS 3 11.977 11.674 0.715 1.00 0.00
H
ATOM 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
H
ATOM 52 C HIS 3 11.761 6.487 0.002 1.00 0.00
C
ATOM 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-d748b
> Source 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.mdp
> define = -DFLEXIBLE
> integrator = md
> nsteps = 0
> dt = 0.001
> constraints = none
> emtol = 10.0
> emstep = 0.01
> nstcomm = 1
> ns_type = simple
> nstlist = 0
> rlist = 0
> rcoulomb = 0
> rvdw = 0
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 1
> pbc = no
> nstlog = 1
> nstenergy = 1
> nstvout = 1
> nstfout = 1
> nstxtcout = 1
> comm_mode = ANGULAR
> continuation = yes
> EOF
>
> 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.arn
> Opening 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 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
> -- gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
> archive at http://www.gromacs.org/search before posting! Please don't post
> (un)subscribe requests to the list. Use the www interface or send it to
> gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> 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 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
> -- gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
> archive at http://www.gromacs.org/search before posting! Please don't post
> (un)subscribe requests to the list. Use the www interface or send it to
> gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> -- gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
> archive at http://www.gromacs.org/search before posting! Please don't post
> (un)subscribe requests to the list. Use the www interface or send it to
> gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
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<<
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100824/f5ea953a/attachment.html>
More information about the gromacs.org_gmx-users
mailing list