[gmx-users] errors with charmm36 ?
Manu Vajpai
manuvajpai at gmail.com
Tue Jan 14 16:53:18 CET 2014
Hi,
Check your position restraints defined in the itp/top file for the lipid
molecules and if they correctly reflect the keywords in the MDP file.
One reason for the second warning might be that the order of appearance of
your lipids and other atoms is not the same between the top and the
PDB/GRO. You can try using grep to arrange the lipids, water and, if exist,
protein atoms in the same order as the PDB. Then perform residue
renumbering by using resnr with editconf to get a new rearranged and
renumbered coordinate file. This should fix the error.
Regards,
Manu Vajpai
On Tue, Jan 14, 2014 at 7:25 PM, hubert santuz <hubert.santuz at gmail.com>wrote:
> Hi,
>
> I just came across this issue a few days ago (with charmm-gui also).
> In fact, atoms C13, C14 and C15 should be just after the C12 atoms in the
> pdb (to match the itp file).
>
> Here a piece of code that I used to retrieve the good order for all POPC
> molecules in your gro file (on unix platform) :
>
> for i in `grep "POPC C13" yourfile.gro --line-number | awk -F: '{print
> $1}'`
> do
> j=$((i-3))
> (echo "${i}m${j}"; echo w; echo q ) | ed yourfile.gro
> done
>
> Basically, ed is used to move each line "POPC C13", 3 lines above. (6
> lines for C14 and 9 lines for C15).
>
> Beware also that a certain number of atom's name are wrong also :
> "0C21" (charmm-gui file) --> 'C210' (itp file)
> "1H10" --> 'H101'
> etc.
> In this case, 'sed' is a great tool ;)
>
> Cheers,
> Hubert
>
>
> Le 14/01/2014 14:22, Justin Lemkul a écrit :
>
>
>>
>> On 1/14/14, 6:41 AM, Albert wrote:
>>
>>> Hello:
>>>
>>> I am trying to equilibrate a membrane system which contains both POPC
>>> and POPG.
>>> I generate the system with charmm-gui, and I try to minimize it in
>>> Gromacs. Here
>>> is my em.mdp file:
>>>
>>> define = -DPOSRES_POPC -DPOSRES_POPG
>>> constraints = none
>>> integrator = steep
>>> dt = 0.001
>>> nsteps = 50000
>>> nstlist = 1.0
>>> ns_type = grid
>>> rlist = 1.0
>>> coulombtype = PME
>>> rcoulomb = 1.0
>>> vdwtype = cutoff
>>> rvdw = 1.0
>>> optimize_fft = yes
>>> emtol = 800.0
>>> emstep = 0.01
>>> pbc = xyz
>>> cutoff-scheme = Verlet
>>>
>>> It said the following:
>>>
>>> -----------------------------------------------------------------------------------------
>>>
>>>
>>> WARNING 1 [file em.mdp, line 18]:
>>> Unknown left-hand 'define' in parameter file
>>>
>>>
>> This error suggests you have a malformatted .mdp file, so make sure you
>> have no hidden characters and are always using a plain-text editor.
>>
>> Warning: atom name 3 in topol.top and merge.pdb does not match (C13 -
>>> H12A)
>>> Warning: atom name 4 in topol.top and merge.pdb does not match (C14 -
>>> H12B)
>>> Warning: atom name 5 in topol.top and merge.pdb does not match (C15 -
>>> C13)
>>> Warning: atom name 6 in topol.top and merge.pdb does not match (H12A -
>>> H13A)
>>> Warning: atom name 7 in topol.top and merge.pdb does not match (H12B -
>>> H13B)
>>> Warning: atom name 8 in topol.top and merge.pdb does not match (H13A -
>>> H13C)
>>> Warning: atom name 9 in topol.top and merge.pdb does not match (H13B -
>>> C14)
>>> Warning: atom name 10 in topol.top and merge.pdb does not match (H13C -
>>> H14A)
>>> Warning: atom name 11 in topol.top and merge.pdb does not match (H14A -
>>> H14B)
>>> Warning: atom name 12 in topol.top and merge.pdb does not match (H14B -
>>> H14C)
>>> Warning: atom name 13 in topol.top and merge.pdb does not match (H14C -
>>> C15)
>>> (more than 20 non-matching atom names)
>>>
>>> WARNING 2 [file topol.top, line 1308]:
>>> 30017 non-matching atom names
>>> atom names from topol.top will be used
>>> atom names from merge.pdb will be ignored
>>> -----------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> I am using Gromacs-4.6.5. I am just wondering why the warning 1 appears?
>>> For Warning 2, I checked the name in my pdb file and the one from
>>> charmm36.ff,
>>> they are consistent with each other. I don't understand why the atom name
>>> doesn't match with each other.
>>>
>>>
>> The topology lists atoms in a different order than the input coordinate
>> file. From the topology you show below, atom 3 should be C13, but in the
>> coordinate file, atom 3 is H12A.
>>
>> -Justin
>>
>> Here is my topol.top file:
>>>
>>>
>>> -----------------------------------------------------------------------------------------
>>>
>>>
>>> ; Include forcefield parameters
>>> #include "charmm36.ff/forcefield.itp"
>>> #include "popg.itp"
>>>
>>> [ moleculetype ]
>>> ; Name nrexcl
>>> POPC 3
>>>
>>> [ atoms ]
>>> ; nr type resnr residue atom cgnr charge mass typeB
>>> chargeB massB
>>> ; residue 1 POPC rtp POPC q 0.0
>>> 1 NTL 1 POPC N 1 -0.6 14.007 ;
>>> qtot -0.6
>>> 2 CTL2 1 POPC C12 2 -0.1 12.011 ;
>>> qtot -0.7
>>> 3 CTL5 1 POPC C13 3 -0.35 12.011 ;
>>> qtot -1.05
>>> 4 CTL5 1 POPC C14 4 -0.35 12.011 ;
>>> qtot -1.4
>>> .
>>> .
>>> .
>>> ; Include Position restraint file
>>> #ifdef POSRES_POPC
>>> #include "popc.itp"
>>> #endif
>>>
>>> ; Include water topology
>>> #include "charmm36.ff/tip3p.itp"
>>>
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ; i funct fcx fcy fcz
>>> 1 1 1000 1000 1000
>>> #endif
>>>
>>> ; Include topology for ions
>>> #include "charmm36.ff/ions.itp"
>>>
>>> [ system ]
>>> ; Name
>>> PCPG
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> POPC 112
>>> POPG 28
>>> SOL 9595
>>> -----------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> thank you very much.
>>>
>>> Albert
>>>
>>
>>
>
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