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

[A. mohammadzadeh]

i used output file that made by charmm-gui for gromacs  but gave me the
same error.

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>