Hi Sir,
Let me share the details of the problem.
I'm currently using Amber18. I modeled the glycolipid structure and ran commands as below;
antechamber -i glu1.pdb -fi pdb -o glu1_new.pdb -fo pdb -c bcc -s 2 -j 5 -at sybyl -dr no
antechamber -fi pdb -fo prepi -i glu1_new.pdb -o glu1.prepi -j 5 -c bcc -at amber
I edited the atomtypes in the prepi file according to GLYCAM06j (for the glucose headgroup) and Lipid17 (for the alkyl chain).
The I ran this commands ;
parmchk2 -i new3_glu1.prepi -f prepi -o frcmod2.frcmod -a Y -p $AMBERHOME/dat/leap/parm/GLYCAM_06j.dat
grep -v "ATTN" frcmod2.frcmod > frcmod2a.frcmod
parmchk2 -i new3_glu1.prepi -f prepi -o frcmod3.frcmod -a Y -p $AMBERHOME/dat/leap/parm/lipid17.dat
grep -v "ATTN" frcmod3.frcmod > frcmod3a.frcmod
And I ran tleap using this command.
tleap -f leaprc.GLYCAM_06j-1
source leaprc.lipid17
loadamberprep glu1.prepi
loadamberparams frcmod2a.frcmod
loadamberparams frcmod3a.frcmod
glu1=loadpdb NEWPDB.PDB
saveamberparm glu1 glu1_trial1.parm7 glu1_trial1.rst7
Here are the error I got when I tried to save the parameter ;
> source leaprc.lipid17
----- Source: /mnt/d/Project_PhD/Amber/amber18/dat/leap/cmd/leaprc.lipid17
----- Source of /mnt/d/Project_PhD/Amber/amber18/dat/leap/cmd/leaprc.lipid17 done
Log file: ./leap.log
Loading parameters: /mnt/d/Project_PhD/Amber/amber18/dat/leap/parm/lipid17.dat
Reading title:
AMBER Lipid17 v1.1 Force Field, A. Skjevik, C. Dickson, B. Madej, I.R. Gould, R.C. Walker*
Loading library: /mnt/d/Project_PhD/Amber/amber18/dat/leap/lib/lipid17.lib
> loadamberprep new2_glu1.prepi
Loading Prep file: ./new2_glu1.prepi
> loadamberparams glu1_trial3_2a_clean.frcmod
Loading parameters: ./glu1_trial3_2a_clean.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadamberparams glu1_trial3_2b_clean.frcmod
Loading parameters: ./glu1_trial3_2b_clean.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> glu1=loadpdb NEWPDB.PDB
Loading PDB file: ./NEWPDB.PDB
total atoms in file: 48
> saveamberparm glu1 glu1_trial4.parm7 glu1_trial4.rst7
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Error: Could not find angle parameter: Os - cA - hA
Error: Could not find angle parameter: Os - cA - hA
Error: Could not find angle parameter: Os - cA - cA
Building proper torsion parameters.
Error: ** No torsion terms for Os-cA-cA-hA
Error: ** No torsion terms for Os-cA-cA-hA
Error: ** No torsion terms for Os-cA-cA-cA
Error: ** No torsion terms for Cg-Os-cA-hA
Error: ** No torsion terms for Cg-Os-cA-hA
Error: ** No torsion terms for Cg-Os-cA-cA
Error: ** No torsion terms for Os-Cg-Os-cA
Building improper torsion parameters.
old PREP-specified impropers:
total 0 improper torsions applied
0 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.
>
I'd like to inquire where can I can the information for the missing parameters.
Thank you so much!
Rae,
University of Malaya,
Malaysia
________________________________
From: Razil Tahir <raziltahir.hotmail.com>
Sent: Wednesday, July 22, 2020 12:03 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Undefined angle parameter and torsion terms in Antechamber
Undefined angle parameter and tortion terms
Hi Amber expert.
I'm currently trying to build glycolipid (glucose with alkyl chain) topology using GLYCAM06 and Lipid17 force field.
When I ran saveamberparm to save the parameter in xleap, I got this error :
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Error: Could not find angle parameter: Os - cA - hA
Error: Could not find angle parameter: Os - cA - hA
Error: Could not find angle parameter: Os - cA - cA
Building proper torsion parameters.
Error: ** No torsion terms for Os-cA-cA-hA
Error: ** No torsion terms for Os-cA-cA-hA
Error: ** No torsion terms for Os-cA-cA-cA
Error: ** No torsion terms for Cg-Os-cA-hA
Error: ** No torsion terms for Cg-Os-cA-hA
Error: ** No torsion terms for Cg-Os-cA-cA
Error: ** No torsion terms for Os-Cg-Os-cA
Based on my humble understanding, this error seems to be revolving around the Oxygen in the glycosidic linkage which I put Os as the atomtype taken from GLYCAM06.
It looks like the the information for angles and tortion terms involving atomtypes from two different force field seem to cause this error.
My question is where can I get these information? Both GLYCAM06 and Lipid17 seem not to have these information.
Thank you in advance.
Rae,
University of Malaya,
Malaysia
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Received on Wed Jul 22 2020 - 08:30:03 PDT
