[gmx-users] dna with charmm36

[gromacs query]

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.


thanks

JIom




On Wed, Feb 5, 2014 at 3:53 PM, gromacs query <gromacsquery at gmail.com>wrote:

> need a coffee!
>
>
> On Wed, Feb 5, 2014 at 3:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/5/14, 10:42 AM, gromacs query wrote:
>>
>>> Hi Justin
>>>
>>> I forgot to ask about waters. With charmm36 it give these options:
>>>
>>>   1: TIP3P   TIP 3-point, recommended, by default uses CHARMM TIP3 with
>>> LJ on H
>>>   2: TIP4P   TIP 4-point
>>>   3: TIP5P   TIP 5-point
>>>   4: SPC     simple point charge
>>>   5: SPC/E   extended simple point charge
>>>   6: None
>>>
>>>
>>> I want to use TIPs3P water (so called Charmm TIP3P). So if I select
>>> option
>>> 1:TIP3P it will be simple TIP3P without LJs on H (please correct me).
>>> How to
>>> force default option which is CHARMM TIP3 with LJs on Hs?
>>>
>>>
>> Incorrect - read the description again.  CHARMM TIP3P is default when
>> using CHARMM.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> 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
>>
>> ==================================================
>>
>
>