[gmx-users] pdb2gmx error with addition of terminal group
anu chandra
anu80125 at gmail.com
Wed Jul 8 15:28:18 CEST 2015
Thanks Justin. Its working fine.
On Wed, Jul 8, 2015 at 12:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/8/15 6:39 AM, anu chandra wrote:
>
>> Dear Gromacs users,
>>
>> I am trying to use pdb2gmx tool to generate topology for my membrane
>> protein system with chamrm36 force field. I have downloaded Gromacs
>> compatible Chamrmm36ff from
>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the
>> N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group
>> attached
>> to the respective terminals. As shown below, I have named the residue/atom
>> names according to the one present in 'merged.rtp' in the charmm36ff file.
>>
>>
>> *******************************************************************************
>> ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00
>> PROA
>> ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00
>> PROA
>> ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00
>> PROA
>> ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00
>> PROA
>> ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00
>> PROA
>> ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00
>> PROA
>> ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00
>> PROA
>> ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00
>> PROA
>> ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00
>> PROA
>> ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00
>> PROA
>> ------------------------------------
>> ------------------------------------
>> ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00
>> PROA
>> ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02
>> PROA
>> ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04
>> PROA
>> ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03
>> PROA
>> ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00
>> PROA
>> ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04
>> PROA
>> ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04
>> PROA
>> ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04
>> PROA
>> ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06
>> PROA
>>
>> ***********************************************************************************
>>
>> But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for
>> the terminal, the pogram terminate with following error
>>
>>
>> ***********************************************************************************
>> Back Off! I just backed up topol.top to ./#topol.top#
>> Processing chain 1 (2607 atoms, 167 residues)
>> Identified residue ACE1 as a starting terminus.
>> Warning: Residue NMA166 in chain has different type (Other) from starting
>> residue ACE1 (Protein).
>> Identified residue SER165 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Special Atom Distance matrix:
>> CYS64 CYS72 CYS95 MET100 CYS101
>> SG1007 SG1123 SG1473 SD1554 SG1568
>> CYS72 SG1123 0.857
>> CYS95 SG1473 2.147 1.806
>> MET100 SD1554 2.390 1.830 0.806
>> CYS101 SG1568 1.896 1.488 0.334 0.773
>> MET143 SD2232 1.844 1.750 1.858 2.389 1.687
>> Select start terminus type for ACE-1
>> 0: NH3+
>> 1: NH2
>> 2: 5TER
>> 3: None
>> 3
>> Start terminus ACE-1: None
>> Select end terminus type for SER-165
>> 0: COO-
>> 1: COOH
>> 2: CT2
>> 3: 3TER
>> 4: None
>> 4
>> End terminus SER-165: None
>>
>> -------------------------------------------------------
>> Program gmx, VERSION 5.0.4
>> Source code file:
>> /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
>>
>> Fatal error:
>> *There is a dangling bond at at least one of the terminal ends. Fix your
>> coordinate file, add a new terminal database entry (.tdb), or select the
>> proper existing terminal entry.*
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> **************************************************************************************
>>
>> Can anybody help me to figure out what is wrong with my input pdb file?
>>
>>
> Note that pdb2gmx finds Ser instead of NMA as the last residue. The clue
> is:
>
> " Warning: Residue NMA166 in chain has different type (Other) from
> starting residue ACE1 (Protein)"
>
> You need to add NMA as "Protein" in residuetypes.dat. You don't want a
> non-patched terminus on Ser, you want a non-patched terminus on NMA.
>
> -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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