[gmx-users] Use dihedraltype 4 to allow several multiplicity terms

[Justin Lemkul]

On 5/5/15 8:09 AM, A. mohammadzadeh wrote:
> i used output file that made by charmm-gui for gromacs  but gave me the
> same error.
>

For the purpose of completing the thread:  Do not modify any topology file 
provided by CHARMM-GUI.  In this case, the OP #included another force field and 
broke the format.  CHARMM-GUI provides self-consistent force field files that 
rely on nothing else.

-Justin

> On Tue, May 5, 2015 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/5/15 7:35 AM, A. mohammadzadeh wrote:
>>
>>> Hello. i have a problem  could you help me to
>>> solve it pleas?
>>>
>>>
>>> i used charmm server to get the parameters for my new membrane with dppc
>>> and cholestrol -
>>>
>>> i converted it into the gromacs topology.
>>>
>>>
>> What does "converted" mean?  I'm assuming you're using CHARMM-GUI, but
>> that means you don't need any conversion.  We provide all of the inputs
>> (.mdp, coordinates, topology) that should be used directly.
>>
>>   When I try grompp:
>>>
>>>
>>> WARNING 23 [file charmm36.itp, line 41]:
>>> Overriding atomtype SOD
>>>
>>>
>>> WARNING 24 [file charmm36.itp, line 201]:
>>> Overriding non-bonded parameters,
>>>
>>> old: 0.290767 0.0906104 0.290767 0.0906104 new
>>> CTL1 SOD 1 2.94954293108e-01 9.06104103511e-02
>>>
>>> WARNING 25 [file charmm36.itp, line 222]:
>>> Overriding non-bonded parameters,
>>>
>>> old: 0.290767 0.0906104 0.290767 0.0906104 new
>>> CTL2 SOD 1 2.94954293108e-01 9.06104103511e-02
>>>
>>> WARNING 26 [file charmm36.itp, line 242]:
>>> Overriding non-bonded parameters,
>>>
>>> old: 0.290767 0.0906104 0.290767 0.0906104 new
>>> CTL3 SOD 1 2.94954293108e-01 9.06104103511e-02
>>>
>>> WARNING 27 [file charmm36.itp, line 261]:
>>> Overriding non-bonded parameters,
>>>
>>> old: 0.290767 0.0906104 0.290767 0.0906104 new
>>> CTL5 SOD 1 2.94954293108e-01 9.06104103511e-02
>>>
>>> WARNING 28 [file charmm36.itp, line 498]:
>>> Overriding Proper Dih. parameters.
>>> Use dihedraltype 4 to allow several multiplicity terms.
>>>
>>> old: 180 4.184 1 180 4.184 1
>>> new: CEL1 CEL1 CTL2 CEL1 9 0.000000e+00 4.016640e-01 4
>>>
>>>
>> The solution to the problem depends on what you mean by "converted" above.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================