Hi Oliver!
Thank you for the detailed response! I apologize for the late reply; it's been a rather busy week!
I made the changes that you had mentioned and reformatted the carbohydrate.
I'm still getting an odd error with GROMACS when using the converted topology/coordinate files. Below is how I have formatted my Glycan. Attached is my tleap output.
I'm still unsure if this is a tleap issue (input/output attached) or a conversion issue.
I tried using the perl script glycam2gmx.pl, but it outputs an error (below) that upon searching correlates with a need for the software ptraj, which is no longer included in current versions of ambertools. I assume it needs this software to be able to
The ACPYPE tool I was using also included a fix for negative dihedrals force constants for Glycans: https://github.com/austenb28/ACPYPE_FIX
This tool is able to convert the top/crd files, but they fail during early steps of MD preparation.
If it's not a tleap issue, then I think I might skip the conversion and continue with Amber.
___
Glycam2gmx.pl output
sh: rdparm: command not found
Parsing PDB file lambda.pdb...
boxParams; X: -2000 Y: -2000 Z: -2000
boxAngles; X: 0 Y: 0 Z: 0
found:
0 residues
0 sodium ions
0 chloride ions
0 waters
Use of uninitialized value $ntotalres in printf at ./glycam2gmx.pl line 311.
0 TOTAL residues read
______________
Glycan Format:
HETATM 2190 O1 ROH A 452 17.463 64.844 45.461 1.00 17.62 O
HETATM 2189 C1 2LB A 452 17.907 63.700 46.176 1.00 17.49 C
HETATM 2191 C2 2LB A 452 17.023 62.505 45.843 1.00 16.53 C
HETATM 2193 C3 2LB A 452 17.583 61.243 46.516 1.00 17.53 C
HETATM 2194 O3 2LB A 452 16.850 60.099 46.104 1.00 19.22 O
HETATM 2195 C4 2LB A 452 19.059 61.053 46.160 1.00 16.95 C
HETATM 2196 O4 2LB A 452 19.174 60.798 44.767 1.00 16.23 O
HETATM 2197 C5 2LB A 452 19.819 62.324 46.521 1.00 16.94 C
HETATM 2198 O5 2LB A 452 19.272 63.431 45.796 1.00 16.08 O
HETATM 2199 C6 2LB A 452 21.295 62.261 46.190 1.00 17.28 C
HETATM 2200 O6 2LB A 452 21.974 63.400 46.704 1.00 18.82 O
HETATM 2192 O2 2LB A 452 15.687 62.763 46.319 1.00 17.71 O
HETATM 2179 C1 0fA A 453 14.654 62.317 45.491 1.00 16.96 C
HETATM 2180 C2 0fA A 453 13.301 62.593 46.168 1.00 17.65 C
HETATM 2181 C3 0fA A 453 13.030 64.102 46.218 1.00 18.33 C
HETATM 2182 C4 0fA A 453 13.088 64.679 44.808 1.00 18.96 C
HETATM 2183 C5 0fA A 453 14.463 64.362 44.202 1.00 18.14 C
HETATM 2184 C6 0fA A 453 14.599 64.833 42.775 1.00 19.90 C
HETATM 2185 O2 0fA A 453 13.321 62.070 47.482 1.00 19.87 O
HETATM 2186 O3 0fA A 453 11.751 64.343 46.784 1.00 20.02 O
___________
Thank you again for helping me!
Kind regards,
Aarya Venkat
Graduate Student
University of Georgia
________________________________
From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Oliver Grant <[log in to unmask]>
Sent: Wednesday, October 31, 2018 9:57 AM
To: [log in to unmask]
Subject: Re: Gromacs Glycam tleap issue
Hi again,
I see you have a co-complex, so building the carbohydrate on glycam.org<http://glycam.org> won't help you. Nor will building from sequence. You'll need to reformat the carbohydrate in 1LZJ in GLYCAM nomenclature so that tleap can recognise it and bond it correctly. Try reorganizing the atoms so the autobonding works. Send all the output from tleap if not.
Oliver
On Wed, Oct 31, 2018 at 2:52 PM Oliver Grant <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi Aarya,
Don't use acpype, unless they have explicitly said that they've updated it to work with GLYCAM. Some terms won't get converted.
You can build the structure on glycam.org/cb<http://glycam.org/cb> and click "download all structures". You'll get the parameter and rst files in the zip file.
The sequence command in leap is for building from prep files. You could do it that way if you want. But note it should be: { ROH 2LB 0fA }. 1fA doesn't make sense there. More detailed examples are the amber manual.
If you load try2.pdb into leap, the issue might be that leap will bond the last atom in a residue to the first atom in the next residue, so order the atoms in the PDB file according to how you want the residues to be auto-bonded by leap (i.e. put the O2 as the last entry for residue 2LB), or put TER cards and use the "bond" command (useful for branched carbohydrates). I'd need to see your leap output to help further.
Best,
Oliver
On Wed, Oct 31, 2018 at 2:37 PM Aarya Venkat <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi everyone!
I am attempting to run an MD in GROMACS on a co-crystallized Glycosyltransferase containing a carbohydrate ligand bound.
The ligand is a-L-Fucp-(1-2)-B-D-Galp.
My structure is 1LZJ is from: https://www.rcsb.org/structure/1LZJ
To parametrize this ligand, I am using a combination of tleap and either acpype or Glycam2gmx.pl to convert the amber parm/crd outputs into gromacs format, but neither are giving me working input files (fails at generating ions due to topology incompatibility/Glycam2gmx output finds no residues, where acpype does find residues).
I have attached my ligand/PDB as well as crd and top files from tleap.
I am thinking this may be due to my tleap file. While it outputs the files without error, I am concerned that I am perhaps not including something here.
My code is simply:
####
source leaprc.GLYCAM_06j-1
loadamberprep GLYCAM_06j-1.prep
mol = loadpdb try2.pdb
saveamberparm mol nacc.parm7 nacc.rst7
####
I have seen others build sequences from their tleap.
ie: seq1 = sequence { ROH 2LB 1fA }
I wasn't sure if I had to do this given that I loaded the pdb in. Please let me know if you need any other information. I would appreciate any advice you have. Thank you!
Kind regards,
Aarya Venkat
