From: Tristan Croll (
Date: Sun Feb 23 2014 - 17:48:04 CST

Hi Ivan,

I'm afraid if you want to include this in your simulation you have a fairly steep learning curve ahead of you, in terms of understanding CHARMM force field files, patches, etc. - not to mention in terms of adjusting these files to be run in NAMD. If you're interested in taking on the challenge, there are a number of discussions of it in the namd-l list. The residue name you're looking for is BGLCNA, and the first thing you'll have to do is change this to fit NAMD's 4-character residue name limit (I changed it to BGLN). Then you'll probably find you need to link this to an adjacent protein residue (if it's N-linked to an asparagine, the patch name is NGLB).

However, I suspect that none of this is the cause of the failure in the RATTLE algorithm. This most commonly comes down to a lack of adequate energy minimization prior to starting dynamics.



-----Original Message-----
From: Ivan Gregoretti []
Sent: Monday, 24 February 2014 9:39 AM
To: Tristan Croll; vmd-l list
Subject: Re: vmd-l: psfgen and unknown residue types

Hi Tristan and everybody,

NAG (N-acetyl glucosamine) seems to be tricky case.

I went to and downloaded

Then I decompressed the tar ball and did

find ./toppar -name '*' | sort | tr \\n \\0 | xargs -0 grep --colour 'NAG'
./toppar/non_charmm/par_bms_dec03.inp:CK NAG 340.0 1.410
!G, par_a4 JWK 9/30/91
./toppar/non_charmm/par_bms_dec03.inp:CA NAG 400.0 1.400
!G, JWK, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:CE NAG 350.0 1.365
!Inosine, adm jr., 2/94
./toppar/non_charmm/par_bms_dec03.inp:HB NAG 471.0 1.01
!G, JWK, par_a12 9/30/91
./toppar/non_charmm/par_bms_dec03.inp:CTT NAG 400.0 1.46
!DRL for 1methylguanine
./toppar/non_charmm/par_bms_dec03.inp:CB CK NAG 67.0 109.4
 !G, JWK, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:!!!NAG CK OK 100.0
125.0 !G, par_a4 adm jr., 10/2/91
./toppar/non_charmm/par_bms_dec03.inp:NAG CK OKG 100.0 125.0 !G, DRL
./toppar/non_charmm/par_bms_dec03.inp:NAG CK S 100.0
121.45 ! 80.0 120.6 !TG, DRL, B3LYP/6-31+G** (119.45)
./toppar/non_charmm/par_bms_dec03.inp:NAN CA NAG 70.0 114.8
 20. 2.30 !G, JWK, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:NAG CA NCA 70.0 122.9
 !G, JWK par_49, par_a11 9/30/91
./toppar/non_charmm/par_bms_dec03.inp:HAR CE NAG 35.0
114.75 !Inosine, adm jr., 2/94
./toppar/non_charmm/par_bms_dec03.inp:CK NAG CA 125.0 128.7
 !G, JWK, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:CK NAG CE 125.0 129.7
 !Inosine, adm jr., 2/94
./toppar/non_charmm/par_bms_dec03.inp:CK NAG HB 40.5 114.3
 !G, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:CA NAG HB 40.5 117.0
 !G par_49, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:CE NAG HB 40.5 116.0
 !Inosine, adm jr., 2/94
./toppar/non_charmm/par_bms_dec03.inp:CK NAG CTT 40.5 114.3
 !G, DRL for 1-methylguanine
./toppar/non_charmm/par_bms_dec03.inp:CA NAG CTT 40.5 117.0
 !G, DRL for 1-methylguanine
./toppar/non_charmm/par_bms_dec03.inp:HAT CTT NAG 43.0 111.0
 !G, DRL for 1-methylguanine
./toppar/non_charmm/par_bms_dec03.inp:!!!OK CK NAG HB 3.0
  2 180.0 ! PAR_36, adm jr., 7/24/91
./toppar/non_charmm/par_bms_dec03.inp:OKG CK NAG HB 3.0
2 180.0 !G, DRL
./toppar/non_charmm/par_bms_dec03.inp:NAG CK CB CB 6.0
2 180.0 ! par_49
./toppar/non_charmm/par_bms_dec03.inp:CB CK NAG CA 6.0
2 180.0 ! par_49
./toppar/non_charmm/par_bms_dec03.inp:CK NAG CA NCA 6.0
2 180.0 ! par_49
./toppar/non_charmm/par_bms_dec03.inp:NAG CA NCA CB 6.0
2 180.0 ! par_49
./toppar/non_charmm/par_bms_dec03.inp:NAG CA NAN HNA 2.0
2 180.0 ! par_49
./toppar/non_charmm/par_bms_dec03.inp:HAR CE NAG HB 1.5 2 180.0
./toppar/non_charmm/par_bms_dec03.inp:HAR CE NAG CK 1.5 2 180.0
./toppar/non_charmm/par_bms_dec03.inp:X CK NAG X 0.9
2 180.0 ! par_36
./toppar/non_charmm/par_bms_dec03.inp:X CA NAG X 1.0
2 180.0 ! par_49
./toppar/non_charmm/par_bms_dec03.inp:CA NAG CTT HAT 0.19 3 0.0
!DRL for 1-methylguanine
./toppar/non_charmm/par_bms_dec03.inp:CK NAG CTT HAT 0.19 3 0.0
!DRL for 1-methylguanine
./toppar/non_charmm/par_bms_dec03.inp:HB X X NAG 0.3
0 0.0 !G, JWK par_15
./toppar/non_charmm/par_bms_dec03.inp:HB CE CK NAG 0.8
0 0.0 !Inosine, adm jr., 2/94
./toppar/non_charmm/par_bms_dec03.inp:CTT X X NAG 20.0
0 0.0 !G, DRL for 1-methylguanine
./toppar/non_charmm/par_bms_dec03.inp:NAG 0.0 -0.20 1.85
./toppar/non_charmm/top_bms_dec03.inp:MASS 20 NAG 14.007000 !
Nucleic acid protonated ring nitrogen, gua N1
./toppar/non_charmm/top_bms_dec03.inp:ATOM N1 NAG -0.5053 !-0.59
./toppar/non_charmm/top_bms_dec03.inp:ATOM N1 NAG -0.4787
./toppar/non_charmm/top_bms_dec03.inp:ATOM N1 NAG -0.3635
./toppar/non_charmm/top_bms_dec03.inp:ATOM N1 NAG -0.1325 !-0.5053
./toppar/param19.inp:FE NR 65.0 1.98! FROM NAGAI ET AL(1980)

or, simply

find ./toppar -name '*' | sort | tr \\n \\0 | xargs -0 grep -l --colour 'NAG'

The only matches to NAG are in the non-CHARMM topologies and
parameters. The accompanying ./toppar/00toppar_file_format.txt says

"subdirectory non_charmm: Contains toppar files for AMBER,
Bristol-Myers Squibb (BMS) and OPLS force fields along with stream
files for a variety of water models. These files have been tested
to the extent that they may be considered reliable representations of
the original force fields, though potentially not exact
representations. These files are NOT maintained and, thus, use at
your own risk. See the 00readme files and note that AMBER requires a
special version of CHARMM as described in the 00readme file."

So, it seems that there is no CHARMM for NAG, not even in CHARMM 36.

I tried running namd excluding the NAG. It did run but after a few
steps namd's log reports:

"...ERROR: Constraint failure in RATTLE algorithm for atom 86!
ERROR: Constraint failure; simulation has become unstable."

I reckon that NAG is needed to keep the three peptide chains together.

More ideas?

Thank you,


Ivan Gregoretti, PhD

On Sun, Feb 23, 2014 at 3:41 AM, Tristan Croll <> wrote:
> "NAG" is N-acetyl glucosamine - probably a glycan linked to an asparagine residue. If you want to keep this in your models, you'll have to use a forcefield that supports glycans, such as CHARMM-36. "HOH" is, of course, water. If all you want is a standard protein simulation, just delete all segnames not starting with P during AutoPSF.
> Tristan Croll
> Lecturer
> Faculty of Science and Technology
> Institute of Health and Biomedical Engineering
> Queensland University of Technology
> 60 Musk Ave
> Kelvin Grove QLD 4059 Australia
> +61 7 3138 6443
> This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.
>> On 23 Feb 2014, at 10:26 am, "Ivan Gregoretti" <> wrote:
>> When running psfgen I get two complains for the "A" chain of 3GRW:
>> ...
>> unknown residue type NAG
>> unknown residue type HOH
>> ...
>> Info: generating structure...psfgen) unknown residue type NAG
>> failed!
>> ERROR: failed on end of segment
>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>> ...
>> Could anybody point me to a document to read and figure out a solution?
>> Thank you,
>> Ivan
>> Ivan Gregoretti, PhD
>> Bioinformatics