[gmx-users] Regarding Residue..

Wed Mar 8 18:21:11 CET 2017

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..

Thank you..

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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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-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.