Project

General

Profile

Bug #587

pdb2gmx error with aromatic vsites and charmm27

Added by R. Bryn almost 7 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
mdrun
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

I have tried to calculate the vsites with the option aromatic using charmm27 and no solvent and have hit a problem with the amino acid tyrosine.

to repeat the bug:

pdb2gmx -f test.gro -vsite aromatic -ignh -ff charmm27 -water none

...

Identified residue TYR2 as a starting terminus.
Identified residue TYR2 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus: NH3+
End terminus: COO-
Opening force field file /opt/gromacs45/share/gromacs/top/charmm27.ff/aminoacids.arn
Checking for duplicate atoms....
Now there are 1 residues with 24 atoms
Making bonds...
Number of bonds was 24, now 24

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.1
Source code file: gen_vsite.c, line: 445

Fatal error:
Dummy mass type (MW) not found in atom type database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

...

here is the file test.gro

Test
21
2TYR N 927 5.792 -7.649 0.694
2TYR H 928 5.790 -7.742 0.660
2TYR CA 929 5.669 -7.568 0.690
2TYR HA 930 5.701 -7.474 0.698
2TYR CB 931 5.595 -7.591 0.559
2TYR HB1 932 5.587 -7.690 0.541
2TYR HB2 933 5.503 -7.551 0.564
2TYR CG 934 5.671 -7.527 0.446
2TYR CD1 935 5.661 -7.388 0.427
2TYR HD1 936 5.605 -7.333 0.488
2TYR CE1 937 5.731 -7.327 0.322
2TYR HE1 938 5.725 -7.229 0.308
2TYR CZ 939 5.810 -7.405 0.237
2TYR OH 940 5.879 -7.345 0.133
2TYR HH 941 5.930 -7.415 0.082
2TYR CD2 942 5.749 -7.604 0.361
2TYR HD2 943 5.756 -7.703 0.375
2TYR CE2 944 5.819 -7.543 0.256
2TYR HE2 945 5.876 -7.599 0.195
2TYR C 946 5.576 -7.603 0.806
2TYR O 947 5.459 -7.565 0.805

Associated revisions

Revision b23037c8 (diff)
Added by Erik Lindahl over 3 years ago

Added dummy mass for charmm TYR aromatic vsites

pdb2gmx was not able to create aromatic vsites
for charmm27 since this dummy mass center was missing.
Note that aromatic vsites are still largely untested,
and not recommended for general usage.

Fixes #587.

Change-Id: Ic7d2976536c6269d1dcf12b7d33bddab096c353f

History

#1 Updated by R. Bryn almost 7 years ago

I was able to get past this problem by modifying the shared forcefield file:

$PATH_TO_GROMACS/share/gromacs/top/charmm27.ff/atomtypes.atp

to include the line,

MW 0.0 ; Dummy mass in rigid tyrosine rings

which appears in:

$PATH_TO_GROMACS/share/gromacs/top/oplsaa.ff/atomtypes.atp

This should be checked with someone who knows this forcefield to check that it is the right change.

#2 Updated by Roland Schulz almost 7 years ago

this looks correct to me. Pär do you agree?

#3 Updated by David van der Spoel almost 7 years ago

It may pass through pdb2gmx, but we're actually trying to discourage aromatic v-sites as they have not been tested well (until someone recently has brushed up the implementation).

#4 Updated by Erik Lindahl almost 7 years ago

Hi David: They've partly been 'brushed up' - with the new 4FDN type they at least conserve (1) energy and (2) structure of some small proteins when run with GB.

I still wouldn't recommend them for general simulations since they're not tested enough, but at least they are no longer obviously broken :-)

#5 Updated by R. Bryn almost 7 years ago

I think that there might be another problem with a non-bonded parameter missing for this atom as well. I am not sure if this should be a new bug or a continuation.

These had to be added to get it to resolve further errors:

in ffnonbonded.itp:

; special dummy-type particles
...
MW 0 0.000000 0.00 A 0.0 0.0

in gb.itp:

MW 0 0 0 0 0 ; vsite (aromatic)

#6 Updated by Rossen Apostolov about 6 years ago

  • Description updated (diff)
  • Assignee deleted (Erik Lindahl)
  • Target version deleted (git master)

#7 Updated by Roland Schulz almost 5 years ago

  • Priority changed from Normal to Low

Given that aromatic isn't recommended I change it it priority low.

#8 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #587.
Uploader: Erik Lindahl ()
Change-Id: Ic7d2976536c6269d1dcf12b7d33bddab096c353f
Gerrit URL: https://gerrit.gromacs.org/3576

#9 Updated by Erik Lindahl over 3 years ago

  • Status changed from New to Fix uploaded
  • Affected version set to 4.6.x

#10 Updated by Erik Lindahl over 3 years ago

  • Status changed from Fix uploaded to Resolved
  • % Done changed from 0 to 100

#11 Updated by Erik Lindahl over 3 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF