Re: [gmx-users] Question Regarding Hydrogen Database Error

2017-02-04 Thread Elise White 
Dr. Lemkul,

Thank you very much for you help!

I just modified my aminoacids.rtp file and my .hdb file as you suggested
and tried running the protein through pdb2gmx just to ensure there weren't
any other errors.

Unfortunately, another error message has popped up now which says,
"Residue 48 named NMA of a molecule in the input file was mapped to an
entry in the topology database, but the atom CH3 used in that entry is not
found in the input file."

Do you have any suggestions as to how I can avoid this? I have attached
the full error message below.

  gmx pdb2gmx -f 2MZ7_AA.pdb -o 2MZ7_AA.gro -ignh -ter -ff gromos53a6_atb
-water spc



Using the Gromos53a6_atb force field in directory gromos53a6_atb.ff


Opening force field file /usr/local/bin/../Cellar/
gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.r2b

Reading 2MZ7_AA.pdb...

WARNING: all CONECT records are ignored

Read 'STRUCTURE OF TAU(267-312) BOUND TO MICROTUBULES', 347 atoms

Analyzing pdb file

Splitting chemical chains based on TER records or chain id changing.

There are 1 chains and 0 blocks of water and 48 residues with 347 atoms


  chain  #res #atoms

  1 'A'48347


All occupancies are one

Opening force field file /usr/local/bin/../Cellar/
gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/atomtypes.atp

Atomtype 64

Reading residue database... (gromos53a6_atb)

Opening force field file /usr/local/bin/../Cellar/
gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.rtp

Using default: not generating all possible dihedrals

Using default: excluding 3 bonded neighbors

Using default: generating 1,4 H--H interactions

Using default: removing proper dihedrals found on the same bond as a proper
dihedral

Residue 109

Sorting it all out...

Opening force field file /usr/local/bin/../Cellar/
gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.hdb

Opening force field file /usr/local/bin/../Cellar/
gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.n.tdb

Opening force field file /usr/local/bin/../Cellar/
gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.c.tdb


Back Off! I just backed up topol.top to ./#topol.top.2#

Processing chain 1 'A' (347 atoms, 48 residues)

Analysing hydrogen-bonding network for automated assignment of histidine

 protonation. 71 donors and 63 acceptors were found.

There are 95 hydrogen bonds

Will use HISE for residue 268

Will use HISE for residue 299

Identified residue ACE266 as a starting terminus.

Identified residue NMA312 as a ending terminus.

8 out of 8 lines of specbond.dat converted successfully

Special Atom Distance matrix:

  HIS268  CYS291

   NE222   SG192

  CYS291   SG192   1.498

  HIS299  NE2254   2.400   1.077

Select start terminus type for ACE-266

 0: NH3+

 1: NH2

 2: None

2

Start terminus ACE-266: None

Select end terminus type for NMA-312

 0: COO-

 1: COOH

 2: None

2

End terminus NMA-312: None

Checking for duplicate atoms

Generating any missing hydrogen atoms and/or adding termini.


---

Program gmx pdb2gmx, VERSION 5.1.1

Source code file: /tmp/gromacs-20160831-84924-1rfxk36/gromacs-5.1.1/src/
gromacs/gmxpreprocess/pgutil.c, line: 127


Fatal error:

Residue 48 named NMA of a molecule in the input file was mapped

to an entry in the topology database, but the atom CH3 used in

that entry is not found in the input file.
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Re: [gmx-users] Topology error

2017-02-04 Thread Justin Lemkul 



On 2/4/17 1:03 AM, Mehreen Jan wrote:

Hello, I want to simulate heme of hemoglobin.I am using Gromacs version
5.0.7. and force feild  GROMOS 96 43a1 and spc water model.I built Heme
topology on Prodrg and Swiss param but Prodrg doesnt accept heme while Swiss
param give errors. Kindly tell me appropriate force feild which I should use
and How to generate iron and oxygen topology? or any alternative which I
should use.Heme topology is available in almost all force feilds but It is
for FE2+ not for FE3+ and I want to simulate FE3+. If it is possible, kindly
please generate topology for heme containing oxygen. I shall be really very
thankful to you.



You should not need external servers to generate a heme topology; GROMOS already 
supports it.  It's called HEME and it's in the .rtp file.  Connections to 
ligating residues should be recognized via existing entries in specbond.dat.


It seems that multiple people are asking the same question, so hopefully 
everyone interested sees this post to avoid repetition.


-Justin


This is the ligand , the heme atom.

HETATM 2341 FE   HEM C1542   7.320  80.715  -5.955  1.00 25.63
Fe HETATM 2342  CHA HEM C1542   7.828  77.591  -5.047  1.00 23.39
C HETATM 2343  CHB HEM C1542   6.501  81.578  -2.733  1.00 23.47
C HETATM 2344  CHC HEM C1542   6.798  84.039  -6.886  1.00 22.00
C HETATM 2345  CHD HEM C1542   7.415  79.872  -9.275  1.00 20.35
C HETATM 2346  NA  HEM C1542   7.232  79.764  -4.194  1.00 25.04
N HETATM 2347  C1A HEM C1542   7.469  78.413  -3.980  1.00 25.77
C HETATM 2348  C2A HEM C1542   7.236  78.109  -2.602  1.00 26.75
C HETATM 2349  C3A HEM C1542   6.841  79.239  -1.971  1.00 26.16
C HETATM 2350  C4A HEM C1542   6.845  80.286  -2.956  1.00 24.77
C HETATM 2351  CMA HEM C1542   6.512  79.509  -0.487  1.00 23.24
C HETATM 2352  CAA HEM C1542   7.389  76.695  -1.990  1.00 30.57
C HETATM 2353  CBA HEM C1542   8.749  76.200  -1.503  1.00 34.82
C HETATM 2354  CGA HEM C1542   8.827  74.825  -0.843  1.00 37.87
C HETATM 2355  O1A HEM C1542   7.934  73.913  -0.680  1.00 39.74
O HETATM 2356  O2A HEM C1542  10.021  74.626  -0.423  1.00 40.42
O HETATM 2357  NB  HEM C1542   6.751  82.455  -4.998  1.00 23.10
N HETATM 2358  C1B HEM C1542   6.460  82.611  -3.660  1.00 22.37
C HETATM 2359  C2B HEM C1542   6.131  83.997  -3.367  1.00 21.40
C HETATM 2360  C3B HEM C1542   6.235  84.681  -4.510  1.00 21.71
C HETATM 2361  C4B HEM C1542   6.614  83.714  -5.544  1.00 21.85
C HETATM 2362  CMB HEM C1542   5.830  84.540  -1.947  1.00 20.77
C HETATM 2363  CAB HEM C1542   6.009  86.177  -4.817  1.00 20.85
C HETATM 2364  CBB HEM C1542   4.894  86.822  -4.391  1.00 21.93
C HETATM 2365  NC  HEM C1542   7.180  81.751  -7.717  1.00 23.07
N HETATM 2366  C1C HEM C1542   6.859  83.099  -7.910  1.00 21.16
C HETATM 2367  C2C HEM C1542   6.559  83.360  -9.301  1.00 19.55
C HETATM 2368  C3C HEM C1542   6.724  82.197  -9.967  1.00 19.24
C HETATM 2369  C4C HEM C1542   7.132  81.190  -9.023  1.00 21.12
C HETATM 2370  CMC HEM C1542   6.119  84.748  -9.815  1.00 17.45
C HETATM 2371  CAC HEM C1542   6.506  81.891 -11.455  1.00 17.62
C HETATM 2372  CBC HEM C1542   5.616  82.527 -12.236  1.00 18.11
C HETATM 2373  ND  HEM C1542   7.593  79.010  -6.981  1.00 22.41
N HETATM 2374  C1D HEM C1542   7.635  78.876  -8.352  1.00 21.08
C HETATM 2375  C2D HEM C1542   7.835  77.476  -8.654  1.00 21.66
C HETATM 2376  C3D HEM C1542   7.913  76.830  -7.505  1.00 21.01
C HETATM 2377  C4D HEM C1542   7.763  77.760  -6.423  1.00 22.07
C HETATM 2378  CMD HEM C1542   7.919  76.887 -10.102  1.00 20.29
C HETATM 2379  CAD HEM C1542   8.131  75.321  -7.321  1.00 20.98
C HETATM 2380  CBD HEM C1542   6.723  74.752  -7.027  1.00 23.17
C HETATM 2381  CGD HEM C1542   6.768  73.298  -6.794  1.00 24.91
C HETATM 2382  O1D HEM C1542   6.242  72.753  -5.808  1.00 29.44
O HETATM 2383  O2D HEM C1542   7.406  72.657  -7.630  1.00 26.84
O HETATM 2384  HHA HEM C1542   8.236  76.638  -4.744  1.00  0.00
H HETATM 2385  HHB HEM C1542   6.228  81.833  -1.720  1.00  0.00
H HETATM 2386  HHC HEM C1542   6.899  85.082  -7.147  1.00  0.00
H HETATM 2387  HHD HEM C1542   7.471  79.584 -10.314  1.00  0.00
H HETATM 2388 HMA1 HEM C1542   5.559  79.043  -0.235  1.00  0.00
H HETATM 2389 HMA2 HEM C1542   7.298  79.091   0.141  1.00  0.00
H HETATM 2390 HMA3 HEM C1542   6.446  80.584  -0.319  1.00  0.00
H HETATM 2391 HAA2 HEM C1542   7.055  75.989  -2.750  1.00  0.00
H HETATM 2392 HAA3 HEM C1542   6.696  76.625  -1.151  1.00  0.00
H HETATM 2393 HBA2 HEM C1542   9.413  76.181  -2.367  1.00  0.00
H HETATM 2394 HBA3 HEM C1542   9.139  76.933  -0.797  1.00  0.00
H HETATM 2395 HMB1 HEM C1542   6.754  84.582  -1.370  1.00  0.00
H HETATM 2396 HMB2 HEM C1542   5.404  85.541  -2.024  1.00  0.00
H HETATM 2397 HMB3 HEM C1542   5.120  83.880  -1.449

Re: [gmx-users] Question Regarding Hydrogen Database Error

2017-02-04 Thread Justin Lemkul 



On 2/4/17 7:00 PM, Elise White wrote:

Hello everyone,

I am a junior at Binghamton High School amidst researching the Tau protein
through
various biomolecular simulations and studies.

Recently, I introduced the NMA capping group to the force field I am
working with - Gromos96
53a6 - by properly adding it to the residuetypes.dat file and adjusting the
aminoacids.rtp file as
depicted below based on a topology of NMA I generated using the ATB. As far
as I'm concerned, this process was successful, as GROMACS recognized the
capping group.

[ NMA ]
 [ atoms ]
 H H   0.258 1
 N N  -1.331 2
CA   CH3   0.571 3
   1HA H  -0.166 4
   2HA H  -0.166 5
   3HA H  -0.166 6


These charges add up to -1, so something has gone wrong.

Moreover, since Gromos96 is a united-atom force field, I have doubts about 
whether or not there should even be H atoms on this carbon.  The point of a 
capping group is to mimic a peptide bond, and the CH3 is an analog to the 
alpha-carbon of an amino acid.  Gromos96 treats such carbons as uncharged.


You also won't be able to generate H atoms that are named with integers as the 
first character, but again I don't think they should be there.  Their types are 
also wrong, as H is a polar H atom (e.g. -NH or -OH groups) so this isn't 
correct, in addition to the fact that a CH3 atom type means you don't have H 
attached to that carbon.  I'm not sure why ATB would give you such a topology, 
but something seems fishy, starting from the very charges themselves.



 [ bonds ]
 H N
 NCA
CA   1HA
CA   2HA
CA   3HA

 [ angles ]
H NCA
NCA   1HA
NCA   2HA
NCA   3HA
  1HACA   2HA
  1HACA   3HA
  2HACA   3HA

However, an error message popped up notifying me that I need to update the
hydrogen database with the 3 tetrahedral hydrogens attached to the alpha
carbon- 1HA, 2HA, and 3HA.
I read chapter 5.6.4 of the manual thoroughly several times, and I am still
incredibly confused about what a "control atom" is - and am quite unsure
about what "control atoms" I need to specify before adding my 3 tetrahedral
hydrogens.



"Control atoms" are atoms that can be used to define a local geometry, i.e. 
there is a simple internal coordinate builder that adds H atoms based on the 
relative positions of existing atoms.  For CHARMM, our NMA capping group (which 
is named NME to avoid a clash with the N-methylacetamide group) is:


NME 2
1   1   HN  N   -C  CH3
3   4   HH3 CH3 N   -C

I would expect a Gromos96 NMA .rtp file to look more like:

[ NMA ]
 [ atoms ]
 H H   0.310 1
 N N  -0.310 2
CA   CH3   0.000 3
 [ bonds ]
 N H
 N CA

with an .hdb entry of

NMA 1
1   1   H  N   -C  CH3

It should be rather simple.

-Justin


It is my hope that one of you vastly experienced computational biochemists
could point me in the right direction or clarify my understanding.

I appreciate you reading my message - it is truly an honor - I respect and
admire all of you.

Best regards,
Elise White



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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[gmx-users] Question Regarding Hydrogen Database Error

2017-02-04 Thread Elise White 
Hello everyone,

I am a junior at Binghamton High School amidst researching the Tau protein
through
various biomolecular simulations and studies.

Recently, I introduced the NMA capping group to the force field I am
working with - Gromos96
53a6 - by properly adding it to the residuetypes.dat file and adjusting the
aminoacids.rtp file as
depicted below based on a topology of NMA I generated using the ATB. As far
as I'm concerned, this process was successful, as GROMACS recognized the
capping group.

[ NMA ]
 [ atoms ]
 H H   0.258 1
 N N  -1.331 2
CA   CH3   0.571 3
   1HA H  -0.166 4
   2HA H  -0.166 5
   3HA H  -0.166 6
 [ bonds ]
 H N
 NCA
CA   1HA
CA   2HA
CA   3HA

 [ angles ]
H NCA
NCA   1HA
NCA   2HA
NCA   3HA
  1HACA   2HA
  1HACA   3HA
  2HACA   3HA

However, an error message popped up notifying me that I need to update the
hydrogen database with the 3 tetrahedral hydrogens attached to the alpha
carbon- 1HA, 2HA, and 3HA.
I read chapter 5.6.4 of the manual thoroughly several times, and I am still
incredibly confused about what a "control atom" is - and am quite unsure
about what "control atoms" I need to specify before adding my 3 tetrahedral
hydrogens.

It is my hope that one of you vastly experienced computational biochemists
could point me in the right direction or clarify my understanding.

I appreciate you reading my message - it is truly an honor - I respect and
admire all of you.

Best regards,
Elise White
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Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

2017-02-04 Thread Christopher Neale 
Awesome Mark, thanks! It works.

I filed a bug about a nonexistent -clustercenter option mentioned in the v5.1.2 
help file, but the command seems to work anyway for my usage.

Thanks again,
Chris.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: 04 February 2017 07:27:52
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] how to reimage PBC based on distance to a given 
selection without recentering or otherwise changing atomic coordinates

Hi,

I've never really use it myself, but I imagine trjconv -pbc cluster is
useful for this kind of scenario when you want to treat a group of
molecules as indivisible.

Mark

On Sat, 4 Feb 2017 09:33 Christopher Neale 
wrote:

> Dear users:
>
> I have a system in which molecule A is in direct contact with molecule B.
> However, molecule B is imaged in a different periodic cell. What I would
> like to do is to get an image of both molecules in a periodic
> representation in which they actually are in contact (i.e., reimage
> molecule B such that it is closest to molecule A). However, I do not want
> to lose spatial information with e.g. a trjconv -center -pbc mol command.
>
> This is part of a complex automated build procedure and I can get into
> more details if that is useful, but the crux is that I am extracting a
> frame from a simulation, building more atoms onto molecule A, and setting
> up a new simulation. To build onto molecule A, I want to then do a vacuum
> EM before adding it back to the water box, for which I first enlarge the
> vacuum box, and changing box dimensions is messing with the periodicity and
> throwing molecule B away from molecule A in an unrealistic fashion
> (molecule B is a tightly bound ligand).
>
> I could do what I want by breaking each molecule out into its own box,
> checking for contacts, reimaging, and then putting them back together. I
> presume (but have not checked) that I could also do this by making a new
> .itp file in which both molecule A and B are part of the same [ molecule ]
> definition and then running a zero-step mdrun. However, I am writing to see
> if anybody knows how reimage based on a selection (would be a single atom
> in molecule A near the contact between molecule A and B) more elegantly
> with processing tools available in gromacs.
>
> Thank you for your help,
> Chris.
> --
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Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

2017-02-04 Thread Mark Abraham 
Hi,

I've never really use it myself, but I imagine trjconv -pbc cluster is
useful for this kind of scenario when you want to treat a group of
molecules as indivisible.

Mark

On Sat, 4 Feb 2017 09:33 Christopher Neale 
wrote:

> Dear users:
>
> I have a system in which molecule A is in direct contact with molecule B.
> However, molecule B is imaged in a different periodic cell. What I would
> like to do is to get an image of both molecules in a periodic
> representation in which they actually are in contact (i.e., reimage
> molecule B such that it is closest to molecule A). However, I do not want
> to lose spatial information with e.g. a trjconv -center -pbc mol command.
>
> This is part of a complex automated build procedure and I can get into
> more details if that is useful, but the crux is that I am extracting a
> frame from a simulation, building more atoms onto molecule A, and setting
> up a new simulation. To build onto molecule A, I want to then do a vacuum
> EM before adding it back to the water box, for which I first enlarge the
> vacuum box, and changing box dimensions is messing with the periodicity and
> throwing molecule B away from molecule A in an unrealistic fashion
> (molecule B is a tightly bound ligand).
>
> I could do what I want by breaking each molecule out into its own box,
> checking for contacts, reimaging, and then putting them back together. I
> presume (but have not checked) that I could also do this by making a new
> .itp file in which both molecule A and B are part of the same [ molecule ]
> definition and then running a zero-step mdrun. However, I am writing to see
> if anybody knows how reimage based on a selection (would be a single atom
> in molecule A near the contact between molecule A and B) more elegantly
> with processing tools available in gromacs.
>
> Thank you for your help,
> Chris.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

2017-02-04 Thread Qing Lv 
Dear Mark,


I built and ran it on the same machine.
The test conclusion of $builddir/bin/mdrun-test is:
[--] Global test environment tear-down
[==] 24 tests from 8 test cases ran. (5206 ms total)
[  PASSED  ] 24 tests.


I searched the complete test result of mdrun-rest (which is quite long), but 
did not find "SIMD" (or Simd, simd).
Thanks.


Qing


At 2017-02-03 21:12:15, "Mark Abraham"  wrote:
>Hi,
>
>Surprising, but we don't test on (or officially support) Cygwin, so could
>happen. It would be most likely to happen if you built on a different
>machine than you were running on... Does $builddir/bin/mdrun-test pass?
>Does the terminal output mention SIMD?
>
>Mark
>
>On Fri, Feb 3, 2017 at 1:29 PM Qing Lv  wrote:
>
>> Mark,
>>
>>
>> The results are:
>> $ ./simd-test.exe
>> Segmentation fault (core dumped)
>>
>>
>> Thanks,
>> Qing
>>
>>
>> At 2017-02-03 19:46:35, "Mark Abraham"  wrote:
>> >Hi,
>> >
>> >Unlikely, given that the other tests passed. But what is the output from
>> >running that manually, e.g. $builddir/bin/simd-test
>> >
>> >Mark
>> >
>> >On Fri, Feb 3, 2017 at 6:52 AM Qing Lv  wrote:
>> >
>> >> Thank you, Mark. I am now trying to install devtoolset-2.
>> >>
>> >>
>> >> Regarding Cygwin version, I must clarify that, although the compilation
>> is
>> >> successful, I got an error message when performing "make check":
>> >> 95% tests passed, 1 tests failed out of 20
>> >> The following tests FAILED:
>> >> 12 - SimdUnitTests (SEGFAULT)
>> >> Will it be a serious problem?
>> >> Thanks.
>> >>
>> >>
>> >> Qing
>> >>
>> >>
>> >> At 2017-02-03 13:08:50, "Mark Abraham" 
>> wrote:
>> >> >Hi,
>> >> >
>> >> >These are linking errors that look like they are from not linking the
>> >> >appropriate version of the C++ standard library. I highly recommend
>> >> leaving
>> >> >the system libraries alone on redhat systems, and instead compiling
>> with
>> >> >the devtoolset packages.
>> >> >
>> >> >Thanks for the Cygwin report. People often report problems that look
>> like
>> >> >they come from broken systems, and we rarely hear of a resolution.
>> >> >
>> >> >Mark
>> >> >
>> >> >On Fri, 3 Feb 2017 05:55 Qing Lv  wrote:
>> >> >
>> >> >> Hi Colleagues,
>> >> >>
>> >> >>
>> >> >> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a
>> Redhat
>> >> 6.5
>> >> >> server; I have updated GCC compiler and all dependent libraries
>> (tried
>> >> GCC
>> >> >> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC
>> 4.4.7,
>> >> >> which is too old.)
>> >> >> I used the commmand
>> >> >> export CC=gcc
>> >> >> export CXX=gcc
>> >> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>> >> >> # No errors reported till now
>> >> >> make
>> >> >> When 100% completed, I got a lot of error messages like
>> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to
>> >> >> ‘std::runtime_error::what() const’
>> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> >> >> And the error messages finished with
>> >> >> collect2: Error: ld returns 1
>> >> >> make[2]: *** [bin/template] Error 1
>> >> >> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> >> >> make: *** [all] Error 2
>> >> >>
>> >> >>
>> >> >> Any friends can help? Thanks
>> >> >> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.
>> >> >>
>> >> >>
>> >> >> Qing
>> >> >> --
>> >> >> Gromacs Users mailing list
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>> >> >> posting!
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>> >> >> send a mail to gmx-users-requ...@gromacs.org.
>> >> >--
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>>

[gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

2017-02-04 Thread Christopher Neale 
Dear users:

I have a system in which molecule A is in direct contact with molecule B. 
However, molecule B is imaged in a different periodic cell. What I would like 
to do is to get an image of both molecules in a periodic representation in 
which they actually are in contact (i.e., reimage molecule B such that it is 
closest to molecule A). However, I do not want to lose spatial information with 
e.g. a trjconv -center -pbc mol command. 

This is part of a complex automated build procedure and I can get into more 
details if that is useful, but the crux is that I am extracting a frame from a 
simulation, building more atoms onto molecule A, and setting up a new 
simulation. To build onto molecule A, I want to then do a vacuum EM before 
adding it back to the water box, for which I first enlarge the vacuum box, and 
changing box dimensions is messing with the periodicity and throwing molecule B 
away from molecule A in an unrealistic fashion (molecule B is a tightly bound 
ligand).

I could do what I want by breaking each molecule out into its own box, checking 
for contacts, reimaging, and then putting them back together. I presume (but 
have not checked) that I could also do this by making a new .itp file in which 
both molecule A and B are part of the same [ molecule ] definition and then 
running a zero-step mdrun. However, I am writing to see if anybody knows how 
reimage based on a selection (would be a single atom in molecule A near the 
contact between molecule A and B) more elegantly with processing tools 
available in gromacs.

Thank you for your help,
Chris.
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