On 1/22/14, 1:06 PM, Sidath Wijesinghe wrote:
  Justin,

i was able to generate  the .top file for 3 monomers by making the corresponding
.rtp entry.

below   is a segment of my .rtp entry and thr .pdb file i used.

.rtp entry for first few atoms out of 208

[ UNK ]
  [ atoms ]

C1      opls_240        0       1
C2      opls_145        -0.12   1
C3      opls_240        0       1
C4      opls_240        0       1
C5      opls_158        -0.12   1
C6      opls_158        -0.12   1
C7      opls_158        -0.12   1
C8      opls_158        -0.12   1
C9      opls_158        -0.12   1
C10     opls_158        -0.12   1


I can almost guarantee that charge group is inappropriately large. Charge groups generally have no more than 3-4 atoms (see the manual).

  [ bonds ]
C1      C2
C1      C13
C1      C82
C2      C3
C2      H28
C3      C4
C3      C5
C4      C11
C4      C21
C5      C6
C5      H29

and so on....

segment of my .pdb used.
ATOM      1 C1    UNK     1     -0.3884 0.71623 0.01741  1.00  0.00      UNK
ATOM      2 C2    UNK     1     0.52009 1.96858 0.02142  1.00  0.00      UNK
ATOM      3 C3    UNK     1     2.05261  1.8016 0.02832  1.00  0.00      UNK
ATOM      4 C4    UNK     1     2.67378 0.39693 0.04493  1.00  0.00      UNK
ATOM      5 C5    UNK     1     3.00381 3.01293 0.02021  1.00  0.00      UNK
ATOM      6 C6    UNK     1     2.43967 4.44371 0.06547  1.00  0.00      UNK
ATOM      7 C7    UNK     1     3.74954 5.25409 0.04830  1.00  0.00      UNK
ATOM      8 C8    UNK     1     3.66193 6.78984 0.08175  1.00  0.00      UNK
ATOM      9 C9    UNK     1     5.14612 7.20376 0.05800  1.00  0.00      UNK
ATOM     10 C10   UNK     1     5.41193  8.7194 0.08617  1.00  0.00      UNK
ATOM     11 C11   UNK     1     4.20533 0.24061 0.06162  1.00  0.00      UNK
ATOM     12 C12   UNK     1     5.73704 0.08685 0.07550  1.00  0.00      UNK
ATOM     13 C13   UNK     1     0.24354 -0.6927 0.01957  1.00  0.00      UNK
ATOM     14 C14   UNK     1     -0.6215 -1.9681 0.00425  1.00  0.00      UNK
ATOM     15 C15   UNK     1     -2.1484 -1.7855 0.06322  1.00  0.00      UNK


i was able to get the .gro and .top file using pdb2gmx

after that i was using grompp but i got an error message as follows.

ERROR 254 [file topol.top, line 1941]:
   No default Ryckaert-Bell. types


ERROR 255 [file topol.top, line 1942]:
   No default Ryckaert-Bell. types


ERROR 256 [file topol.top, line 1943]:
   No default Ryckaert-Bell. types
i was reading the gmx_users blogs and it specifies that i need to manually enter
the parameters that have errors.

i am not clear with that. could you please tell me what i need to do here. (
when i look the lines regarding the errors  they
are pointing out the diheadrals)


You need to check those lines for what the atom types are for those atoms. Parameters are not present in ffbonded.itp for that sequence of atoms so you need to add suitable parameters.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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