[gmx-users] Regarding Residue..
Justin Lemkul
jalemkul at vt.edu
Wed Mar 8 19:27:06 CET 2017
On 3/8/17 12:21 PM, Dilip H N wrote:
> I want to simulate a liquid having Charmm FF with inserting a small
> dipeptide as above FF into it...
> whn i gave the command gmx pdb2gmx and selected the charmm FF..
> I am getting the following error...
>
> All occupancies are one
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/atomtypes.atp
> Atomtype 412
> Reading residue database... (charmm36-nov2016)
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.rtp
> Residue 1025
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.c.tdb
> Warning: Starting residue AMM11 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM12 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM13 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM14 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMM15 in chain not identified as Protein/RNA/DNA.
> More than 5 unidentified residues at start of chain - disabling further
> warnings.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn
> Checking for duplicate atoms....
> Now there are 1031 atoms. Deleted 3 duplicates.
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 257 residues with 1031 atoms
> Making bonds...
> Number of bonds was 774, now 774
> Generating angles, dihedrals and pairs...
> Before cleaning: 6 pairs
>
> -------------------------------------------------------
> Program: gmx pdb2gmx, version 2016.2
> Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 148)
>
> Fatal error:
> Residue 257 named AMM1 of a molecule in the input file was mapped
> to an entry in the topology database, but the atom C used in
> an interaction of type improper in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
> How can i solve this problem..
>
Since AMM1 is ammonia (NH3) and there are no impropers or carbon atoms in it,
this suggests you have instructed pdb2gmx to construct protein termini on the
AMM1 "chain" of molecules. You haven't provided the full screen output,
including these selections, but I suspect this is the case.
I recommend making things simpler by processing only the peptide with pdb2gmx,
and treating the ammonia like any other solvent molecule. Generate the topology
for a single molecule separately and #include it like you would for the
"typical" protocol with water.
-Justin
> Thank you..
>
>
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
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>
> On Wed, Mar 8, 2017 at 6:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/8/17 6:18 AM, Dilip H N wrote:
>>
>>> I have created a glycylglycine.pdb using avogadro software..and its
>>> residue
>>> are..
>>>
>>> N DGLY A
>>>
>>> CA DGLY A
>>>
>>> C DGLY A
>>>
>>> O DGLY A
>>>
>>> HA1 DGLY A
>>>
>>> HA2 DGLY A
>>>
>>> H DGLY A
>>>
>>> HN DGLY A
>>>
>>> N DGLY A
>>>
>>> CA DGLY A
>>>
>>> C DGLY A
>>>
>>> O DGLY A
>>> HA1 DGLY A
>>> HA2 DGLY A
>>>
>>> H DGLY A
>>>
>>> OXT DGLY A
>>>
>>> HO DGLY A
>>>
>>> But i intended for charmm FF whr residues are written as
>>>
>>> [DGLY]
>>> [ atoms ]
>>> N NH1 -0.470 0
>>> HN H 0.310 1
>>> CA CT2 -0.020 2
>>> HA1 HB2 0.090 3
>>> HA2 HB2 0.090 4
>>> C C 0.510 5
>>> O O -0.510 6
>>>
>>> Hw can i correlate my .pdb file residue with charmmFF36 residue..??
>>>
>>> and in glycylglycine there are total of 17 atoms but in charmm FF thr
>>> are only 7 atomic residues described as shown..
>>>
>>>
>> They're different things. Amino acids prefixed with "D" in CHARMM are
>> D-amino acids, e.g. inverted C-alpha stereochemistry from those typically
>> found in nature. Thus, DGLY is not appropriate here (of course, glycine is
>> not chiral, but we have a DGLY version for atom type consistency).
>>
>> Glycylglycine is just Gly-Gly, so you don't need a special residue for it;
>> glycine is already in every protein force field (and shouldn't be named
>> DGLY, anyway).
>>
>> How can i solve this problem..?? wht does OXT,HO describe..?? to which
>>> atom..
>>>
>>>
>> Have you visualized the structure and labeled its atoms? The first step
>> in any simulation process is using your eyes :) Then think about what the
>> normal biochemistry of amino acids is.
>>
>> -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
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