[gmx-users] dna with charmm36

[gromacs query]

Hi Justin
Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5
replaced by D* and D*3 by D* otherwise it ends with errors as said
previously.

thanks
JIom


On Tue, Mar 4, 2014 at 1:00 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/3/14, 7:57 PM, gromacs query wrote:
>
>> Hi All
>>
>> Its in continuation. I am confused about something. In PDB file obtained
>> from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them.
>> PDB has DC5 as starting and DT3 as end residue and I get this error:
>>
>> pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or
>> without
>> -ignh)
>>
>> WARNING: atom H3' is missing in residue DC5 1 in the pdb file
>>
>>           You might need to add atom H3' to the hydrogen database of
>> building block DC5
>>
>>           in the file merged.hdb (see the manual)
>>
>>
>>
>> WARNING: atom H5'1 is missing in residue DT3 10 in the pdb file
>>
>>           You might need to add atom H5'1 to the hydrogen database of
>> building block DT3
>>
>>           in the file merged.hdb (see the manual)
>>
>>
>>
>> I found DC5 and others (D*5 and D*3) are missing in merged.hdb. Are these
>> missing or intentionally not added? Also if I change name of DC5 to DC and
>> DT3 to DT it works fine and all Hs are added without error.
>>
>>
> Specific naming of terminal residues like this is not needed for CHARMM.
>  Just choose the correct termini (5TER and 3TER) and they will be patched
> appropriately.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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.
>