[gmx-users] Angles not read
jalemkul at vt.edu
Mon Jun 10 14:42:34 CEST 2013
On 6/10/13 8:40 AM, Steven Neumann wrote:
> On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 6/10/13 8:23 AM, Steven Neumann wrote:
>>> Dear Gmx Users,
>>> I created my own CG force field and i process my structure to pdb2gmx. I
>>> process 3 beads I created to check whether the topology is properly
>>> Using the CG force field in directory ./CG.ff
>>> No file 'watermodels.dat' found, will not include a water model
>>> Reading 60central_Carbons.pdb...
>>> Read 3 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 3 residues with 3 atoms
>>> chain #res #atoms
>>> 1 'X' 3 3
>>> All occupancy fields zero. This is probably not an X-Ray structure
>>> Opening force field file ./CG.ff/atomtypes.atp
>>> Atomtype 1
>>> Reading residue database... (CG)
>>> Opening force field file ./CG.ff/aminoacids.rtp
>>> Reading .rtp file without '[ bondedtypes ]' directive,
>>> Will proceed as if the entry
>>> [ bondedtypes ]
>>> ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14
>>> 1 1 1 2 0 3 1
>>> Residue 13t at the beginning of ./CG.ff/aminoacids.rtp
>>> Sorting it all out...
>>> Back Off! I just backed up topol.top to ./#topol.top.2#
>>> Processing chain 1 'X' (3 atoms, 3 residues)
>>> Identified residue MET1 as a starting terminus.
>>> Identified residue VAL3 as a ending terminus.
>>> 8 out of 8 lines of specbond.dat converted successfully
>>> Checking for duplicate atoms....
>>> Now there are 3 residues with 3 atoms
>>> Making bonds...
>>> No bonds
>>> Generating angles, dihedrals and pairs...
>>> Making cmap torsions...There are 0 dihedrals, 0 impropers, 0
>>> 0 pairs, 0 bonds and 0 virtual sites
>>> Total mass 319.420 a.m.u.
>>> Total charge 1.000 e
>>> Writing topology
>>> Back Off! I just backed up posre.itp to ./#posre.itp.2#
>>> Writing coordinate file...
>>> Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2#
>>> --------- PLEASE NOTE ------------
>>> You have successfully generated a topology from:3Carbons.pdb.
>>> The CG force field is used.
>>> --------- ETON ESAELP ------------
>>> gcq#304: "Gabba Gabba Hey!" (The Ramones)
>>> It stated that there are no angles.
>>> However in my ffbonded.itp which i ncluded in my forcefield.itp
>>> [ angletypes ]
>>> ; i j k funct th0 C0 C1 C2 C3 C4
>>> CME CSE CVA 6 0 0.0680894 -0.0328291000 590330
>>> -46.3 13
>>> How Gromacs can read this angle?
>> [angletypes] simply define possible interactions, but are not used unless
>> there are [angles] in the .rtp that use them. pdb2gmx writes angles based
>> on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot
>> write any angles. Does your .rtp entry specify [angles] but no [bonds]?
> I want to use constraints with SHAKE as bonds...no harmonic bonds. In this
> case pdb2gmx will never create angles? Shall I also manually add [ angles ]
> to my top then?
Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored.
>> In terms of bonds I want to use constraints, can I use in my ffbonded.itp
>>> costrainttypes] or add them automatically after?
>> You would need [constraints] in your .top file, not [constrainttypes]
>> (same hierarchy as described above with angles). Usually .mdp keywords
>> serve better than topology modifications in the case of constraints, unless
>> you're only constraining a subset of atoms within a single [moleculetype].
> I can manually add [ constraints ] to my top after processing with pdb2gmx
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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