[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Berk Hess gmx3 at hotmail.com
Wed Aug 25 15:36:16 CEST 2010


You can find the residue name to rtp translation table in:
share/top/amber99.ff/aminoacids.r2b

I don't have a list with Amber names and funtions for the amino acids.
Currently for Amber in Gromacs we have CYS (standard, neutral, protonated)
and CYX (disulfide bond).
Does Amber use CYP instead of CYS?

Berk

From: alanwilter at gmail.com
Date: Wed, 25 Aug 2010 14:17:58 +0100
Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
To: gmx-users at gromacs.org

Just one more question. How are you handling CYS? In amber it could be CYP, CYN etc.

Thanks a lot,
Alan
On 25 August 2010 13:59, Berk Hess <gmx3 at hotmail.com> wrote:







Hi,

I now turned on the automatic HIE, and analogous, terminal renaming on by default.

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: Wed, 25 Aug 2010 14:34:30 +0200








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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>>http://www.bio.cam.ac.uk/~awd28<<







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>>http://www.bio.cam.ac.uk/~awd28<<





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>>http://www.bio.cam.ac.uk/~awd28<<



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